analyze_results.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import sys\n",
    "import psycopg2\n",
    "from sqlalchemy import create_engine\n",
    "from io import StringIO\n",
    "import pandas as pd\n",
    "import csv\n",
    "up_one =  (os.path.abspath(os.path.join(os.getcwd(), os.pardir)))\n",
    "sys.path.append(up_one)\n",
    "up_two =  (os.path.abspath(os.path.join(os.getcwd(), os.pardir, os.pardir)))\n",
    "sys.path.append(up_two)\n",
    "#from minorlab import metapdb\n",
    "import subprocess\n",
    "from collections import defaultdict\n",
    "from tqdm.notebook import trange, tqdm\n",
    "import re\n",
    "import numpy as np\n",
    "\n",
    "import pprint\n",
    "pp = pprint.PrettyPrinter(indent=4)\n",
    "pp1 = pprint.PrettyPrinter(indent=4, depth=1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Appris files and function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "appris = pd.read_csv('Data/appris_transcript_names.tsv', sep='\\t', header=None, names=['gene','ref'])\n",
    "nonappris = pd.read_csv('Data/not_appris_transcript_names.tsv', sep='\\t', header=None, names=['gene','notref'])\n",
    "def ref_nonref(gene):\n",
    "    ref = appris.loc [ appris['gene']== gene]['ref'].tolist()\n",
    "    #print (ref)\n",
    "    non_ref = nonappris.loc [nonappris['gene']==gene]['notref'].tolist()\n",
    "    non_ref.sort()\n",
    "    #print (non_ref)\n",
    "    return (ref, non_ref)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>gene</th>\n",
       "      <th>ref</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DDX11L2</td>\n",
       "      <td>DDX11L2-202</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>DDX11L2</td>\n",
       "      <td>DDX11L2-201</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>DDX11L1</td>\n",
       "      <td>DDX11L1-201</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>WASH7P</td>\n",
       "      <td>WASH7P-201</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>MIR6859-1</td>\n",
       "      <td>MIR6859-1-201</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>80225</th>\n",
       "      <td>MT-ND6</td>\n",
       "      <td>MT-ND6-201</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>80226</th>\n",
       "      <td>MT-TE</td>\n",
       "      <td>MT-TE-201</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>80227</th>\n",
       "      <td>MT-CYB</td>\n",
       "      <td>MT-CYB-201</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>80228</th>\n",
       "      <td>MT-TT</td>\n",
       "      <td>MT-TT-201</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>80229</th>\n",
       "      <td>MT-TP</td>\n",
       "      <td>MT-TP-201</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>80230 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            gene            ref\n",
       "0        DDX11L2    DDX11L2-202\n",
       "1        DDX11L2    DDX11L2-201\n",
       "2        DDX11L1    DDX11L1-201\n",
       "3         WASH7P     WASH7P-201\n",
       "4      MIR6859-1  MIR6859-1-201\n",
       "...          ...            ...\n",
       "80225     MT-ND6     MT-ND6-201\n",
       "80226      MT-TE      MT-TE-201\n",
       "80227     MT-CYB     MT-CYB-201\n",
       "80228      MT-TT      MT-TT-201\n",
       "80229      MT-TP      MT-TP-201\n",
       "\n",
       "[80230 rows x 2 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "appris"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(['CD44-206'], ['CD44-201', 'CD44-202', 'CD44-203', 'CD44-204', 'CD44-205', 'CD44-207', 'CD44-208', 'CD44-209', 'CD44-210', 'CD44-211', 'CD44-212', 'CD44-213', 'CD44-214', 'CD44-215', 'CD44-216', 'CD44-217', 'CD44-218', 'CD44-219', 'CD44-220', 'CD44-221', 'CD44-222', 'CD44-223', 'CD44-224', 'CD44-225', 'CD44-226', 'CD44-227', 'CD44-228', 'CD44-229', 'CD44-230', 'CD44-231', 'CD44-232', 'CD44-233', 'CD44-234', 'CD44-235', 'CD44-236', 'CD44-237', 'CD44-238'])\n"
     ]
    }
   ],
   "source": [
    "print (ref_nonref('CD44'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Genes related to SMC differentiation\n",
    "with open ('Data/temp_list.txt') as f:\n",
    "    ff = set(f.read().splitlines())\n",
    "print (ff)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Read all Blast into DataFrame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>qseqid</th>\n",
       "      <th>qlen</th>\n",
       "      <th>qstart</th>\n",
       "      <th>qend</th>\n",
       "      <th>sseqid</th>\n",
       "      <th>slen</th>\n",
       "      <th>sstart</th>\n",
       "      <th>send</th>\n",
       "      <th>evalue</th>\n",
       "      <th>bitscore</th>\n",
       "      <th>length</th>\n",
       "      <th>nident</th>\n",
       "      <th>gaps</th>\n",
       "      <th>gapopen</th>\n",
       "      <th>mismatch</th>\n",
       "      <th>pident</th>\n",
       "      <th>gene</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>7evw_R</td>\n",
       "      <td>599</td>\n",
       "      <td>36</td>\n",
       "      <td>574</td>\n",
       "      <td>FZD1-201</td>\n",
       "      <td>647</td>\n",
       "      <td>103</td>\n",
       "      <td>647</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>905.0</td>\n",
       "      <td>551</td>\n",
       "      <td>440</td>\n",
       "      <td>18</td>\n",
       "      <td>6</td>\n",
       "      <td>93</td>\n",
       "      <td>79.855</td>\n",
       "      <td>FZD1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>7evw_R</td>\n",
       "      <td>599</td>\n",
       "      <td>38</td>\n",
       "      <td>574</td>\n",
       "      <td>FZD2-201</td>\n",
       "      <td>565</td>\n",
       "      <td>28</td>\n",
       "      <td>565</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>893.0</td>\n",
       "      <td>553</td>\n",
       "      <td>434</td>\n",
       "      <td>31</td>\n",
       "      <td>3</td>\n",
       "      <td>88</td>\n",
       "      <td>78.481</td>\n",
       "      <td>FZD2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>7evw_R</td>\n",
       "      <td>599</td>\n",
       "      <td>49</td>\n",
       "      <td>563</td>\n",
       "      <td>FZD5-201</td>\n",
       "      <td>585</td>\n",
       "      <td>33</td>\n",
       "      <td>536</td>\n",
       "      <td>2.420000e-180</td>\n",
       "      <td>523.0</td>\n",
       "      <td>533</td>\n",
       "      <td>276</td>\n",
       "      <td>47</td>\n",
       "      <td>14</td>\n",
       "      <td>210</td>\n",
       "      <td>51.782</td>\n",
       "      <td>FZD5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>7evw_R</td>\n",
       "      <td>599</td>\n",
       "      <td>44</td>\n",
       "      <td>589</td>\n",
       "      <td>FZD10-201</td>\n",
       "      <td>581</td>\n",
       "      <td>29</td>\n",
       "      <td>573</td>\n",
       "      <td>1.480000e-165</td>\n",
       "      <td>485.0</td>\n",
       "      <td>562</td>\n",
       "      <td>261</td>\n",
       "      <td>33</td>\n",
       "      <td>10</td>\n",
       "      <td>268</td>\n",
       "      <td>46.441</td>\n",
       "      <td>FZD10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>7evw_R</td>\n",
       "      <td>599</td>\n",
       "      <td>49</td>\n",
       "      <td>562</td>\n",
       "      <td>FZD3-201</td>\n",
       "      <td>666</td>\n",
       "      <td>28</td>\n",
       "      <td>512</td>\n",
       "      <td>2.230000e-162</td>\n",
       "      <td>480.0</td>\n",
       "      <td>515</td>\n",
       "      <td>236</td>\n",
       "      <td>31</td>\n",
       "      <td>3</td>\n",
       "      <td>248</td>\n",
       "      <td>45.825</td>\n",
       "      <td>FZD3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1909511</th>\n",
       "      <td>2z9a_A,B</td>\n",
       "      <td>88</td>\n",
       "      <td>3</td>\n",
       "      <td>81</td>\n",
       "      <td>PSAP-201</td>\n",
       "      <td>524</td>\n",
       "      <td>311</td>\n",
       "      <td>389</td>\n",
       "      <td>7.630000e-47</td>\n",
       "      <td>157.0</td>\n",
       "      <td>79</td>\n",
       "      <td>79</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>PSAP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1909512</th>\n",
       "      <td>2z9a_A,B</td>\n",
       "      <td>88</td>\n",
       "      <td>3</td>\n",
       "      <td>55</td>\n",
       "      <td>PSAP-204</td>\n",
       "      <td>167</td>\n",
       "      <td>115</td>\n",
       "      <td>167</td>\n",
       "      <td>4.070000e-31</td>\n",
       "      <td>108.0</td>\n",
       "      <td>53</td>\n",
       "      <td>53</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>PSAP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1909513</th>\n",
       "      <td>8d58_A</td>\n",
       "      <td>246</td>\n",
       "      <td>1</td>\n",
       "      <td>246</td>\n",
       "      <td>METTL1-202</td>\n",
       "      <td>276</td>\n",
       "      <td>20</td>\n",
       "      <td>265</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>516.0</td>\n",
       "      <td>246</td>\n",
       "      <td>246</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>METTL1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1909514</th>\n",
       "      <td>8d58_A</td>\n",
       "      <td>246</td>\n",
       "      <td>104</td>\n",
       "      <td>240</td>\n",
       "      <td>METTL1-204</td>\n",
       "      <td>124</td>\n",
       "      <td>2</td>\n",
       "      <td>124</td>\n",
       "      <td>3.650000e-85</td>\n",
       "      <td>250.0</td>\n",
       "      <td>137</td>\n",
       "      <td>123</td>\n",
       "      <td>14</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>89.781</td>\n",
       "      <td>METTL1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1909515</th>\n",
       "      <td>8d58_A</td>\n",
       "      <td>246</td>\n",
       "      <td>1</td>\n",
       "      <td>74</td>\n",
       "      <td>METTL1-201</td>\n",
       "      <td>155</td>\n",
       "      <td>20</td>\n",
       "      <td>93</td>\n",
       "      <td>1.550000e-48</td>\n",
       "      <td>158.0</td>\n",
       "      <td>74</td>\n",
       "      <td>72</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>97.297</td>\n",
       "      <td>METTL1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1909442 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "           qseqid  qlen  qstart  qend      sseqid  slen  sstart  send  \\\n",
       "1          7evw_R   599      36   574    FZD1-201   647     103   647   \n",
       "2          7evw_R   599      38   574    FZD2-201   565      28   565   \n",
       "3          7evw_R   599      49   563    FZD5-201   585      33   536   \n",
       "4          7evw_R   599      44   589   FZD10-201   581      29   573   \n",
       "5          7evw_R   599      49   562    FZD3-201   666      28   512   \n",
       "...           ...   ...     ...   ...         ...   ...     ...   ...   \n",
       "1909511  2z9a_A,B    88       3    81    PSAP-201   524     311   389   \n",
       "1909512  2z9a_A,B    88       3    55    PSAP-204   167     115   167   \n",
       "1909513    8d58_A   246       1   246  METTL1-202   276      20   265   \n",
       "1909514    8d58_A   246     104   240  METTL1-204   124       2   124   \n",
       "1909515    8d58_A   246       1    74  METTL1-201   155      20    93   \n",
       "\n",
       "                evalue  bitscore  length  nident  gaps  gapopen  mismatch  \\\n",
       "1         0.000000e+00     905.0     551     440    18        6        93   \n",
       "2         0.000000e+00     893.0     553     434    31        3        88   \n",
       "3        2.420000e-180     523.0     533     276    47       14       210   \n",
       "4        1.480000e-165     485.0     562     261    33       10       268   \n",
       "5        2.230000e-162     480.0     515     236    31        3       248   \n",
       "...                ...       ...     ...     ...   ...      ...       ...   \n",
       "1909511   7.630000e-47     157.0      79      79     0        0         0   \n",
       "1909512   4.070000e-31     108.0      53      53     0        0         0   \n",
       "1909513   0.000000e+00     516.0     246     246     0        0         0   \n",
       "1909514   3.650000e-85     250.0     137     123    14        1         0   \n",
       "1909515   1.550000e-48     158.0      74      72     0        0         2   \n",
       "\n",
       "          pident    gene  \n",
       "1         79.855    FZD1  \n",
       "2         78.481    FZD2  \n",
       "3         51.782    FZD5  \n",
       "4         46.441   FZD10  \n",
       "5         45.825    FZD3  \n",
       "...          ...     ...  \n",
       "1909511  100.000    PSAP  \n",
       "1909512  100.000    PSAP  \n",
       "1909513  100.000  METTL1  \n",
       "1909514   89.781  METTL1  \n",
       "1909515   97.297  METTL1  \n",
       "\n",
       "[1909442 rows x 17 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## Read in full blast results  - Using version 2\n",
    "# Note version 1 of blast_full_PDB_vs_gencode had some lines that were Warnings\n",
    "columns =  ['qseqid','qlen', 'qstart', 'qend', 'sseqid', 'slen', 'sstart', 'send', 'evalue', 'bitscore', 'length', 'nident', 'gaps','gapopen', 'mismatch', 'pident']\n",
    "blast_df= pd.read_csv('Data/blast_full_PDB_vs_gencode_v2.tsv', sep='\\t', header = 1, names = columns)\n",
    "# Reduce the sseqid to just isoform name\n",
    "gene_hash={}\n",
    "for iso in blast_df['sseqid']:\n",
    "    p = iso.split('|')\n",
    "    gene_hash[p[0]]= p[1].split('.')[0]\n",
    "blast_df['sseqid'] = [ s.split('|')[0] for s in blast_df['sseqid'].to_list()]\n",
    "blast_df['gene'] = [s.split('-')[0] for s in blast_df['sseqid'].to_list()]\n",
    "blast_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "blast_df.loc [blast_df['gene']=='BAZ2B'].sort_values(['qseqid','bitscore'], ascending = False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Read in the results from  max_ref_nonref_bitscores"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdb</th>\n",
       "      <th>top</th>\n",
       "      <th>gene</th>\n",
       "      <th>top_nonref</th>\n",
       "      <th>max_nonref_bs</th>\n",
       "      <th>max_ref_bs</th>\n",
       "      <th>diff</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>6lth_L</td>\n",
       "      <td>4586.0</td>\n",
       "      <td>ARID1A</td>\n",
       "      <td>True</td>\n",
       "      <td>4586.0</td>\n",
       "      <td>3852.0</td>\n",
       "      <td>734.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>7ktr_C</td>\n",
       "      <td>1658.0</td>\n",
       "      <td>SUPT20H</td>\n",
       "      <td>True</td>\n",
       "      <td>1658.0</td>\n",
       "      <td>1163.0</td>\n",
       "      <td>495.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>4kkd_A,B</td>\n",
       "      <td>892.0</td>\n",
       "      <td>MASP1</td>\n",
       "      <td>True</td>\n",
       "      <td>892.0</td>\n",
       "      <td>433.0</td>\n",
       "      <td>459.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>7k36_B,D,E,F,G</td>\n",
       "      <td>1479.0</td>\n",
       "      <td>STRN3</td>\n",
       "      <td>True</td>\n",
       "      <td>1479.0</td>\n",
       "      <td>1046.0</td>\n",
       "      <td>433.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>8fgw_B</td>\n",
       "      <td>2585.0</td>\n",
       "      <td>IFT122</td>\n",
       "      <td>True</td>\n",
       "      <td>2585.0</td>\n",
       "      <td>2155.0</td>\n",
       "      <td>430.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35076</th>\n",
       "      <td>7t3p_A,B,C,D</td>\n",
       "      <td>5445.0</td>\n",
       "      <td>ITPR3</td>\n",
       "      <td>False</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5445.0</td>\n",
       "      <td>-5445.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35077</th>\n",
       "      <td>7u9x_A,B,C,D</td>\n",
       "      <td>10359.0</td>\n",
       "      <td>RYR2</td>\n",
       "      <td>False</td>\n",
       "      <td>4861.0</td>\n",
       "      <td>10359.0</td>\n",
       "      <td>-5498.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35078</th>\n",
       "      <td>7u9q_A,D,B,C</td>\n",
       "      <td>10362.0</td>\n",
       "      <td>RYR2</td>\n",
       "      <td>False</td>\n",
       "      <td>4861.0</td>\n",
       "      <td>10362.0</td>\n",
       "      <td>-5501.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35079</th>\n",
       "      <td>6dqj_A,B,C,D</td>\n",
       "      <td>5566.0</td>\n",
       "      <td>ITPR3</td>\n",
       "      <td>False</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5566.0</td>\n",
       "      <td>-5566.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35080</th>\n",
       "      <td>7mq8_SP</td>\n",
       "      <td>5722.0</td>\n",
       "      <td>UTP20</td>\n",
       "      <td>False</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5722.0</td>\n",
       "      <td>-5722.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>35081 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                  pdb      top     gene  top_nonref  max_nonref_bs  \\\n",
       "0              6lth_L   4586.0   ARID1A        True         4586.0   \n",
       "1              7ktr_C   1658.0  SUPT20H        True         1658.0   \n",
       "2            4kkd_A,B    892.0    MASP1        True          892.0   \n",
       "3      7k36_B,D,E,F,G   1479.0    STRN3        True         1479.0   \n",
       "4              8fgw_B   2585.0   IFT122        True         2585.0   \n",
       "...               ...      ...      ...         ...            ...   \n",
       "35076    7t3p_A,B,C,D   5445.0    ITPR3       False            0.0   \n",
       "35077    7u9x_A,B,C,D  10359.0     RYR2       False         4861.0   \n",
       "35078    7u9q_A,D,B,C  10362.0     RYR2       False         4861.0   \n",
       "35079    6dqj_A,B,C,D   5566.0    ITPR3       False            0.0   \n",
       "35080         7mq8_SP   5722.0    UTP20       False            0.0   \n",
       "\n",
       "       max_ref_bs    diff  \n",
       "0          3852.0   734.0  \n",
       "1          1163.0   495.0  \n",
       "2           433.0   459.0  \n",
       "3          1046.0   433.0  \n",
       "4          2155.0   430.0  \n",
       "...           ...     ...  \n",
       "35076      5445.0 -5445.0  \n",
       "35077     10359.0 -5498.0  \n",
       "35078     10362.0 -5501.0  \n",
       "35079      5566.0 -5566.0  \n",
       "35080      5722.0 -5722.0  \n",
       "\n",
       "[35081 rows x 7 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# read in the results from  max_ref_nonref_bitscores\n",
    "mrnr_df = pd.read_csv('Data/max_ref_nonref_bitscores.tsv', sep = '\\t')\n",
    "mrnr_df = mrnr_df.rename(columns = {'Unnamed: 0':'pdb'})\n",
    "pdb_nonref_list_by_gene = mrnr_df.loc[ mrnr_df['diff'] > 10  ].groupby('gene')['pdb'].apply(list).to_dict()\n",
    "pdb_ref_list_by_gene  = mrnr_df.loc[ mrnr_df['diff'] < 10 ].groupby('gene')['pdb'].apply(list).to_dict()\n",
    "mrnr_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Find genes with both ref and isos¶"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>gene</th>\n",
       "      <th>max</th>\n",
       "      <th>min</th>\n",
       "      <th>diff</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>MASP1</td>\n",
       "      <td>459.0</td>\n",
       "      <td>-412.0</td>\n",
       "      <td>871.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ARID1A</td>\n",
       "      <td>734.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>733.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>KCNN4</td>\n",
       "      <td>79.7</td>\n",
       "      <td>-630.0</td>\n",
       "      <td>709.7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SUPT20H</td>\n",
       "      <td>495.0</td>\n",
       "      <td>-158.0</td>\n",
       "      <td>653.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AFF4</td>\n",
       "      <td>82.0</td>\n",
       "      <td>-563.0</td>\n",
       "      <td>645.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93</th>\n",
       "      <td>CNGA3</td>\n",
       "      <td>54.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>54.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>94</th>\n",
       "      <td>DYSF</td>\n",
       "      <td>53.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>53.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>95</th>\n",
       "      <td>MED25</td>\n",
       "      <td>55.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>51.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>96</th>\n",
       "      <td>NRG1</td>\n",
       "      <td>50.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>50.2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>97</th>\n",
       "      <td>KCNQ2</td>\n",
       "      <td>51.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>45.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>98 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       gene    max    min   diff\n",
       "0     MASP1  459.0 -412.0  871.0\n",
       "1    ARID1A  734.0    1.0  733.0\n",
       "2     KCNN4   79.7 -630.0  709.7\n",
       "3   SUPT20H  495.0 -158.0  653.0\n",
       "4      AFF4   82.0 -563.0  645.0\n",
       "..      ...    ...    ...    ...\n",
       "93    CNGA3   54.0    0.0   54.0\n",
       "94     DYSF   53.0    0.0   53.0\n",
       "95    MED25   55.0    4.0   51.0\n",
       "96     NRG1   50.2    0.0   50.2\n",
       "97    KCNQ2   51.0    6.0   45.0\n",
       "\n",
       "[98 rows x 4 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "both = set(pdb_nonref_list_by_gene).intersection(set(pdb_ref_list_by_gene))\n",
    "#print (both)\n",
    "results = []\n",
    "for gene in list(both):\n",
    "    #print (gene, ref_nonref(gene))\n",
    "    mrnr_df2 = mrnr_df.loc[ mrnr_df['gene']== gene, ['pdb', 'gene', 'max_nonref_bs', 'max_ref_bs', 'diff']]\n",
    "    max = mrnr_df2['diff'].max()\n",
    "    min = mrnr_df2['diff'].min()\n",
    "    #print (f'{gene}\\t{max}\\t{min}\\t{max - min}' )\n",
    "    results.append([gene, max, min, max-min])   \n",
    "    #input ('ready?')   \n",
    "#print (results)\n",
    "mrnr_df3= pd.DataFrame(results, columns = ['gene', 'max', 'min','diff'])\n",
    "check_first= mrnr_df3.loc [mrnr_df3['max'] > 50].sort_values(by='diff',ascending = False).reset_index(drop=True)\n",
    "#check_first.to_excel('Data/check_first.xlsx')\n",
    "check_first"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = check_first.loc[ check_first['gene'] ==  'BAZ2B']\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "check_2nd = mrnr_df3.loc [mrnr_df3['diff'] > 0].sort_values(by='diff',ascending = False).reset_index(drop=True)\n",
    "check_2nd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Read in Chess file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'ENST00000621850': 'CHS.10000.1',\n",
       " 'ENST00000401611': 'CHS.10000.10',\n",
       " 'ENST00000621128': 'CHS.10000.2',\n",
       " 'ENST00000619839': 'CHS.10000.3',\n",
       " 'nan': 'hypothetical.10127.1',\n",
       " 'ENST00000316851': 'CHS.10000.alt102',\n",
       " 'ENST00000531044': 'CHS.10000.5',\n",
       " 'ENST00000611284': 'CHS.10000.51',\n",
       " 'ENST00000529356': 'CHS.10000.alt103',\n",
       " 'ENST00000526322': 'CHS.10000.alt106',\n",
       " 'ENST00000533073': 'CHS.10000.alt107',\n",
       " 'ENST00000524916': 'CHS.10000.alt108',\n",
       " 'ENST00000530090': 'CHS.10000.alt109',\n",
       " 'ENST00000528158': 'CHS.10000.alt110',\n",
       " 'ENST00000529221': 'CHS.10003.alt104',\n",
       " 'ENST00000494714': 'CHS.10003.alt105',\n",
       " 'ENST00000531164': 'CHS.10003.alt103',\n",
       " 'ENST00000464224': 'CHS.10003.alt106',\n",
       " 'ENST00000314756': 'CHS.10003.alt110',\n",
       " 'ENST00000527781': 'CHS.10003.alt111',\n",
       " 'ENST00000525989': 'CHS.10003.alt112',\n",
       " 'ENST00000534793': 'CHS.10003.alt113',\n",
       " 'ENST00000478125': 'CHS.10003.alt114',\n",
       " 'ENST00000480233': 'CHS.10003.alt115',\n",
       " 'ENST00000303941': 'CHS.10004.alt100',\n",
       " 'ENST00000542948': 'CHS.10004.alt101',\n",
       " 'ENST00000544518': 'CHS.10005.10',\n",
       " 'ENST00000346454': 'CHS.10005.3',\n",
       " 'ENST00000362072': 'CHS.10005.alt103',\n",
       " 'ENST00000542968': 'CHS.10005.alt106',\n",
       " 'ENST00000535984': 'CHS.10005.alt107',\n",
       " 'ENST00000539420': 'CHS.10005.alt108',\n",
       " 'ENST00000545579': 'CHS.10008.10',\n",
       " 'ENST00000536856': 'CHS.10008.alt110',\n",
       " 'ENST00000540540': 'CHS.10008.alt112',\n",
       " 'ENST00000544476': 'CHS.10008.6',\n",
       " 'ENST00000538955': 'CHS.10008.7',\n",
       " 'ENST00000544634': 'CHS.10008.8',\n",
       " 'ENST00000299882': 'CHS.10008.alt111',\n",
       " 'ENST00000545265': 'CHS.10008.alt118',\n",
       " 'ENST00000538091': 'CHS.10008.alt119',\n",
       " 'ENST00000200135': 'CHS.10009.alt102',\n",
       " 'ENST00000535142': 'CHS.10009.7',\n",
       " 'ENST00000538209': 'CHS.10009.alt104',\n",
       " 'ENST00000294409': 'CHS.1001.1',\n",
       " 'ENST00000373816': 'CHS.1001.alt101',\n",
       " 'ENST00000361872': 'CHS.1001.3',\n",
       " 'ENST00000480454': 'CHS.1001.alt110',\n",
       " 'ENST00000453129': 'CHS.10010.alt100',\n",
       " 'ENST00000545540': 'CHS.10011.25',\n",
       " 'ENST00000003302': 'CHS.10011.30',\n",
       " 'ENST00000537706': 'CHS.10011.40',\n",
       " 'ENST00000540438': 'CHS.10011.61',\n",
       " 'ENST00000544967': 'CHS.10011.alt110',\n",
       " 'ENST00000544272': 'CHS.10011.alt112',\n",
       " 'ENST00000542033': 'CHS.10011.alt113',\n",
       " 'ENST00000260191': 'CHS.10013.alt101',\n",
       " 'ENST00000537778': 'CHS.10013.4',\n",
       " 'ENST00000543092': 'CHS.10013.alt108',\n",
       " 'ENST00000355556': 'CHS.10014.1',\n",
       " 'ENST00000504030': 'CHS.10014.alt102',\n",
       " 'ENST00000510849': 'CHS.10014.alt103',\n",
       " 'ENST00000299961': 'CHS.10014.4',\n",
       " 'ENST00000506841': 'CHS.10014.alt101',\n",
       " 'ENST00000299964': 'CHS.10019.alt105',\n",
       " 'ENST00000535401': 'CHS.10019.4',\n",
       " 'ENST00000541754': 'CHS.10019.alt106',\n",
       " 'ENST00000545255': 'CHS.10019.alt107',\n",
       " 'ENST00000542507': 'CHS.1002.1',\n",
       " 'ENST00000373812': 'CHS.1002.alt100',\n",
       " 'ENST00000541996': 'CHS.1002.8',\n",
       " 'ENST00000478283': 'CHS.1002.alt102',\n",
       " 'ENST00000684295': 'CHS.10020.12',\n",
       " 'ENST00000683318': 'CHS.10020.13',\n",
       " 'ENST00000392996': 'CHS.10020.14',\n",
       " 'ENST00000682218': 'CHS.10020.alt112',\n",
       " 'ENST00000335953': 'CHS.10020.alt102',\n",
       " 'ENST00000684612': 'CHS.10020.alt103',\n",
       " 'ENST00000682810': 'CHS.10020.alt104',\n",
       " 'ENST00000541602': 'CHS.10020.alt105',\n",
       " 'ENST00000682971': 'CHS.10020.alt106',\n",
       " 'ENST00000682697': 'CHS.10020.alt107',\n",
       " 'ENST00000683554': 'CHS.10020.alt108',\n",
       " 'ENST00000683006': 'CHS.10020.alt110',\n",
       " 'ENST00000535379': 'CHS.10020.alt113',\n",
       " 'ENST00000325636': 'CHS.10026.2',\n",
       " 'ENST00000623205': 'CHS.10026.alt100',\n",
       " 'ENST00000265881': 'CHS.10027.alt102',\n",
       " 'ENST00000538198': 'CHS.10027.alt107',\n",
       " 'ENST00000539754': 'CHS.10027.19',\n",
       " 'ENST00000539275': 'CHS.10027.5',\n",
       " 'ENST00000544010': 'CHS.10027.alt100',\n",
       " 'ENST00000544196': 'CHS.10027.alt101',\n",
       " 'ENST00000539333': 'CHS.10027.alt103',\n",
       " 'ENST00000543243': 'CHS.10027.alt104',\n",
       " 'ENST00000541703': 'CHS.10027.alt105',\n",
       " 'ENST00000543131': 'CHS.10027.alt106',\n",
       " 'ENST00000539119': 'CHS.10027.alt108',\n",
       " 'ENST00000544827': 'CHS.10027.alt109',\n",
       " 'ENST00000546316': 'CHS.10027.alt110',\n",
       " 'ENST00000538791': 'CHS.10027.alt111',\n",
       " 'ENST00000538403': 'CHS.10027.alt112',\n",
       " 'ENST00000540492': 'CHS.10027.alt113',\n",
       " 'ENST00000375490': 'CHS.10028.alt101',\n",
       " 'ENST00000540163': 'CHS.10028.3',\n",
       " 'ENST00000542140': 'CHS.10028.4',\n",
       " 'ENST00000544313': 'CHS.10028.5',\n",
       " 'ENST00000545678': 'CHS.10028.6',\n",
       " 'ENST00000541475': 'CHS.10028.alt100',\n",
       " 'ENST00000389586': 'CHS.10029.alt101',\n",
       " 'ENST00000234961': 'CHS.1003.alt100',\n",
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       " 'ENST00000648516': 'CHS.10373.12',\n",
       " 'ENST00000263579': 'CHS.10373.alt101',\n",
       " 'ENST00000529149': 'CHS.10373.alt105',\n",
       " 'ENST00000444328': 'CHS.10375.alt105',\n",
       " 'ENST00000534083': 'CHS.10375.10',\n",
       " 'ENST00000392669': 'CHS.10375.20',\n",
       " 'ENST00000532243': 'CHS.10375.25',\n",
       " 'ENST00000676545': 'CHS.10375.33',\n",
       " 'ENST00000676867': 'CHS.10375.alt104',\n",
       " 'ENST00000677503': 'CHS.10375.36',\n",
       " 'ENST00000356132': 'CHS.10375.40',\n",
       " 'ENST00000227495': 'CHS.10375.6',\n",
       " 'ENST00000530591': 'CHS.10375.7',\n",
       " 'ENST00000531217': 'CHS.10375.alt101',\n",
       " 'ENST00000678865': 'CHS.10375.alt102',\n",
       " 'ENST00000677721': 'CHS.10375.alt106',\n",
       " 'ENST00000526727': 'CHS.10375.alt111',\n",
       " 'ENST00000676831': 'CHS.10375.alt112',\n",
       " 'ENST00000449406': 'CHS.10375.alt113',\n",
       " 'ENST00000534457': 'CHS.10375.alt114',\n",
       " 'ENST00000524860': 'CHS.10375.alt115',\n",
       " 'ENST00000529097': 'CHS.10376.alt113',\n",
       " 'ENST00000525144': 'CHS.10376.alt101',\n",
       " 'ENST00000525704': 'CHS.10376.18',\n",
       " 'ENST00000533026': 'CHS.10376.alt116',\n",
       " 'ENST00000547738': 'CHS.10376.alt117',\n",
       " 'ENST00000549874': 'CHS.10376.alt118',\n",
       " 'ENST00000378755': 'CHS.104.3',\n",
       " 'ENST00000378756': 'CHS.104.alt104',\n",
       " 'ENST00000536055': 'CHS.104.6',\n",
       " 'ENST00000672388': 'CHS.104.alt105',\n",
       " 'ENST00000429957': 'CHS.104.alt107',\n",
       " 'ENST00000400830': 'CHS.104.alt108',\n",
       " 'ENST00000339394': 'CHS.1040.alt105',\n",
       " 'ENST00000336798': 'CHS.1040.alt108',\n",
       " 'ENST00000535549': 'CHS.10406.5',\n",
       " 'ENST00000319397': 'CHS.10406.6',\n",
       " 'ENST00000392668': 'CHS.10406.alt101',\n",
       " 'ENST00000526145': 'CHS.10406.9',\n",
       " 'ENST00000525404': 'CHS.10406.alt106',\n",
       " 'ENST00000534087': 'CHS.10414.13',\n",
       " 'ENST00000281428': 'CHS.10414.14',\n",
       " 'ENST00000527786': 'CHS.10414.alt110',\n",
       " 'ENST00000344954': 'CHS.10414.3',\n",
       " 'ENST00000527767': 'CHS.10414.alt106',\n",
       " 'ENST00000528790': 'CHS.10414.alt112',\n",
       " 'ENST00000392664': 'CHS.10416.2',\n",
       " 'ENST00000392665': 'CHS.10416.3',\n",
       " 'ENST00000392666': 'CHS.10416.alt102',\n",
       " 'ENST00000440599': 'CHS.10416.5',\n",
       " 'ENST00000324036': 'CHS.10416.6',\n",
       " 'ENST00000257075': 'CHS.1042.4',\n",
       " 'ENST00000498419': 'CHS.1042.alt102',\n",
       " 'ENST00000529846': 'CHS.1042.alt103',\n",
       " 'ENST00000525997': 'CHS.1042.alt104',\n",
       " 'ENST00000525948': 'CHS.1042.alt105',\n",
       " 'ENST00000310799': 'CHS.10420.alt101',\n",
       " 'ENST00000524878': 'CHS.10420.alt102',\n",
       " 'ENST00000338350': 'CHS.10421.14',\n",
       " 'ENST00000529694': 'CHS.10421.alt100',\n",
       " 'ENST00000533599': 'CHS.10421.alt103',\n",
       " 'ENST00000310343': 'CHS.10422.9',\n",
       " 'ENST00000524655': 'CHS.10422.alt108',\n",
       " 'ENST00000534357': 'CHS.10422.alt109',\n",
       " 'ENST00000458238': 'CHS.10423.1',\n",
       " 'ENST00000530777': 'CHS.10423.alt105',\n",
       " 'ENST00000531399': 'CHS.10423.alt106',\n",
       " 'ENST00000602346': 'CHS.10423.9',\n",
       " 'ENST00000527504': 'CHS.10423.alt107',\n",
       " 'ENST00000281437': 'CHS.10427.alt105',\n",
       " 'ENST00000527754': 'CHS.10435.13',\n",
       " 'ENST00000281441': 'CHS.10435.alt100',\n",
       " 'ENST00000529381': 'CHS.10435.alt102',\n",
       " 'ENST00000524567': 'CHS.10435.alt106',\n",
       " 'ENST00000682444': 'CHS.10436.13',\n",
       " 'ENST00000532147': 'CHS.10436.alt102',\n",
       " 'ENST00000530278': 'CHS.10436.alt103',\n",
       " 'ENST00000529319': 'CHS.10436.alt104',\n",
       " 'ENST00000526940': 'CHS.10436.alt105',\n",
       " 'ENST00000527581': 'CHS.10438.alt103',\n",
       " 'ENST00000531431': 'CHS.10438.alt104',\n",
       " 'ENST00000263574': 'CHS.10442.1',\n",
       " 'ENST00000278756': 'CHS.10442.17',\n",
       " 'ENST00000338167': 'CHS.10442.alt101',\n",
       " 'ENST00000528499': 'CHS.10442.3',\n",
       " 'ENST00000345598': 'CHS.10442.4',\n",
       " 'ENST00000533616': 'CHS.10442.alt100',\n",
       " 'ENST00000533860': 'CHS.10442.alt103',\n",
       " 'ENST00000530493': 'CHS.10442.alt104',\n",
       " 'ENST00000278742': 'CHS.10443.alt100',\n",
       " 'ENST00000530532': 'CHS.10443.alt101',\n",
       " 'ENST00000524718': 'CHS.10443.alt102',\n",
       " 'ENST00000530376': 'CHS.10443.alt103',\n",
       " 'ENST00000527478': 'CHS.10446.14',\n",
       " 'ENST00000445008': 'CHS.10446.alt115',\n",
       " 'ENST00000525842': 'CHS.10446.5',\n",
       " 'ENST00000357899': 'CHS.10446.alt108',\n",
       " 'ENST00000530205': 'CHS.10446.alt119',\n",
       " 'ENST00000529982': 'CHS.10446.alt120',\n",
       " 'ENST00000525623': 'CHS.10446.alt121',\n",
       " 'ENST00000528448': 'CHS.10446.alt123',\n",
       " 'ENST00000257359': 'CHS.10448.3',\n",
       " 'ENST00000299164': 'CHS.10449.alt102',\n",
       " 'ENST00000528555': 'CHS.10458.17',\n",
       " 'ENST00000265909': 'CHS.10458.alt101',\n",
       " 'ENST00000530356': 'CHS.10458.45',\n",
       " 'ENST00000533214': 'CHS.10458.47',\n",
       " 'ENST00000527116': 'CHS.10458.alt106',\n",
       " 'ENST00000534726': 'CHS.10458.alt107',\n",
       " 'ENST00000426933': 'CHS.10458.alt108',\n",
       " 'ENST00000533318': 'CHS.10458.alt109',\n",
       " 'ENST00000530330': 'CHS.10458.alt110',\n",
       " 'ENST00000524460': 'CHS.10458.alt112',\n",
       " 'ENST00000527451': 'CHS.10458.alt113',\n",
       " 'ENST00000374791': 'CHS.10467.15',\n",
       " 'ENST00000374784': 'CHS.10467.33',\n",
       " 'ENST00000425719': 'CHS.10467.34',\n",
       " 'ENST00000374786': 'CHS.10467.35',\n",
       " 'ENST00000474900': 'CHS.10467.alt124',\n",
       " 'ENST00000683400': 'CHS.10467.alt104',\n",
       " 'ENST00000436745': 'CHS.10467.alt110',\n",
       " 'ENST00000477098': 'CHS.10467.alt111',\n",
       " 'ENST00000539799': 'CHS.10467.alt121',\n",
       " 'ENST00000427481': 'CHS.10467.alt122',\n",
       " 'ENST00000496094': 'CHS.10467.alt123',\n",
       " 'ENST00000457381': 'CHS.10467.alt125',\n",
       " 'ENST00000373736': 'CHS.1047.alt102',\n",
       " 'ENST00000526106': 'CHS.1047.alt103',\n",
       " 'ENST00000524381': 'CHS.10476.alt101',\n",
       " 'ENST00000331898': 'CHS.10476.6',\n",
       " 'ENST00000374778': 'CHS.10476.8',\n",
       " 'ENST00000529038': 'CHS.10476.9',\n",
       " 'ENST00000525412': 'CHS.10476.alt102',\n",
       " 'ENST00000263694': 'CHS.1048.alt100',\n",
       " 'ENST00000486941': 'CHS.1048.alt102',\n",
       " 'ENST00000489853': 'CHS.1048.alt103',\n",
       " 'ENST00000373720': 'CHS.1048.alt104',\n",
       " 'ENST00000474025': 'CHS.1048.alt105',\n",
       " 'ENST00000463988': 'CHS.1048.alt106',\n",
       " 'ENST00000532889': 'CHS.10483.7',\n",
       " 'ENST00000299140': 'CHS.10483.alt102',\n",
       " 'ENST00000564347': 'CHS.10484.alt100',\n",
       " 'ENST00000526663': 'CHS.10484.alt101',\n",
       " 'ENST00000373714': 'CHS.1049.1',\n",
       " 'ENST00000615916': 'CHS.1049.2',\n",
       " 'ENST00000546109': 'CHS.1049.3',\n",
       " 'ENST00000616859': 'CHS.1049.4',\n",
       " 'ENST00000344147': 'CHS.1049.alt101',\n",
       " 'ENST00000618216': 'CHS.1049.6',\n",
       " 'ENST00000616393': 'CHS.1049.8',\n",
       " 'ENST00000627541': 'CHS.1049.alt102',\n",
       " 'ENST00000299106': 'CHS.10493.alt101',\n",
       " 'ENST00000441717': 'CHS.10493.2',\n",
       " 'ENST00000534549': 'CHS.10493.alt100',\n",
       " 'ENST00000531302': 'CHS.10493.alt102',\n",
       " 'ENST00000524969': 'CHS.10493.alt103',\n",
       " 'ENST00000534548': 'CHS.10496.5',\n",
       " 'ENST00000688672': 'CHS.10496.7',\n",
       " 'ENST00000525964': 'CHS.10496.8',\n",
       " 'ENST00000525432': 'CHS.10496.alt102',\n",
       " 'ENST00000525485': 'CHS.10496.alt103',\n",
       " 'ENST00000526422': 'CHS.10496.alt104',\n",
       " 'ENST00000532445': 'CHS.10496.alt106',\n",
       " 'ENST00000281187': 'CHS.10497.alt101',\n",
       " 'ENST00000532160': 'CHS.10497.alt108',\n",
       " 'ENST00000525918': 'CHS.10497.alt109',\n",
       " 'ENST00000531741': 'CHS.10497.alt110',\n",
       " 'ENST00000531135': 'CHS.10498.10',\n",
       " 'ENST00000392594': 'CHS.10498.2',\n",
       " 'ENST00000352327': 'CHS.10498.3',\n",
       " 'ENST00000392595': 'CHS.10498.4',\n",
       " 'ENST00000341541': 'CHS.10498.alt101',\n",
       " 'ENST00000533975': 'CHS.10498.alt104',\n",
       " 'ENST00000281182': 'CHS.10499.alt116',\n",
       " 'ENST00000531338': 'CHS.10499.34',\n",
       " 'ENST00000374752': 'CHS.10499.alt113',\n",
       " 'ENST00000525961': 'CHS.10499.alt114',\n",
       " 'ENST00000530533': 'CHS.10499.alt115',\n",
       " 'ENST00000533387': 'CHS.10499.alt117',\n",
       " 'ENST00000528325': 'CHS.10499.alt118',\n",
       " 'ENST00000524739': 'CHS.10499.alt119',\n",
       " 'ENST00000378733': 'CHS.105.alt100',\n",
       " 'ENST00000624426': 'CHS.105.alt103',\n",
       " 'ENST00000373713': 'CHS.1050.alt102',\n",
       " 'ENST00000497275': 'CHS.1050.alt104',\n",
       " 'ENST00000498148': 'CHS.1050.alt105',\n",
       " 'ENST00000431683': 'CHS.10501.alt102',\n",
       " 'ENST00000486034': 'CHS.10501.alt116',\n",
       " 'ENST00000498012': 'CHS.10501.alt117',\n",
       " ...}"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "chess_pdb_dir = \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2\"\n",
    "chess_df = pd.read_excel('Data/Chess/iso_all_v1.2.xlsx')\n",
    "chess_df = chess_df.replace('-',np.nan)\n",
    "chess_df['enst'] = [ str(g_id).split('.')[0] for g_id in chess_df['GENCODE ID']]\n",
    "chess_dict = chess_df.set_index('enst')['CHESS ID'].dropna().to_dict()\n",
    "chess_dict"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "chess_dict['ENST00000392783']"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Next few cells adapted from Gloria\n",
    "\n",
    "\n",
    "##### Read in the files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "80169 Appris transcripts\n",
      "141431 non-Appris transcripts\n",
      "1909443 records in Gencode\n"
     ]
    }
   ],
   "source": [
    "# Read in the appris transcripts\n",
    "appris_transcripts = set()\n",
    "with open('Data/appris_transcript_names.tsv', 'r') as appris_file:\n",
    "    appris_reader = csv.reader(appris_file, delimiter='\\t')\n",
    "    for row in appris_reader:\n",
    "        appris_transcripts.add(row[1])\n",
    "    print (f'{len(appris_transcripts)} Appris transcripts')\n",
    "\n",
    "# Read in the nonappris transcripts\n",
    "nonappris_transcripts = set()\n",
    "with open('Data/not_appris_transcript_names.tsv', 'r') as nonappris_file:\n",
    "    nonappris_reader = csv.reader(nonappris_file, delimiter='\\t')\n",
    "    for row in nonappris_reader:\n",
    "        nonappris_transcripts.add(row[1])\n",
    "    print (f'{len(nonappris_transcripts)} non-Appris transcripts')\n",
    "\n",
    "# Read in the PDB to GenCode mapping\n",
    "pdb_to_gencode = []\n",
    "with open('Data/blast_full_PDB_vs_gencode_v2.tsv', 'r') as pdb_file:\n",
    "    pdb_reader = csv.reader(pdb_file, delimiter='\\t')\n",
    "    next(pdb_reader, None)\n",
    "    for row in pdb_reader:\n",
    "        # This makes the sseqid just the isoform name\n",
    "        row[5] = row[5].split('|')[0]\n",
    "        pdb_to_gencode.append(row)\n",
    "    print (f'{len (pdb_to_gencode)} records in Gencode')\n",
    "\n",
    "    \n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Group the PDB to GenCode mappings by qseqid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " This represents 35081 pdbs\n"
     ]
    }
   ],
   "source": [
    "# Group the PDB to GenCode mappings by qseqid\n",
    "# print (pdb_to_gencode[0])\n",
    "pdb_grouped_by_qseqid = {}\n",
    "for row in pdb_to_gencode:\n",
    "    #print (row)\n",
    "    qseqid = row[1]\n",
    "    if qseqid not in pdb_grouped_by_qseqid:\n",
    "        pdb_grouped_by_qseqid[qseqid] = []\n",
    "    pdb_grouped_by_qseqid[qseqid].append(row)\n",
    "print(f' This represents {len(pdb_grouped_by_qseqid)} pdbs')\n",
    "# Below is just a check.\n",
    "#for k in list(pdb_grouped_by_qseqid.keys())[0:2]:\n",
    "#   print (pdb_grouped_by_qseqid[k])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb_grouped_by_qseqid['5wrv_A']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "name_dict= {}\n",
    "name_enst = {}\n",
    "with open ('Data/transcript_list.txt') as file:\n",
    "    transcript_names = file.read().splitlines()\n",
    "for row in transcript_names:\n",
    "    #print (row)\n",
    "    parts=row.split('|')\n",
    "    name_dict[parts[5]] = row\n",
    "    name_enst[parts[5]] = parts[1]\n",
    "#print (name_dict)\n",
    "#print (name_enst)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Filter the PDB to non-appris transcripts\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "filtered_pdb_to_gencode is 8230 long\n"
     ]
    }
   ],
   "source": [
    "# Filter the PDB to non-appris transcripts\n",
    "filtered_pdb_to_gencode = []\n",
    "count = 0\n",
    "genes_with_ref=set()\n",
    "also_refs = defaultdict(set)\n",
    "ref_pdbs = defaultdict(list)\n",
    "for qseqid, pdb_group in pdb_grouped_by_qseqid.items():\n",
    "    #if pdb_group[0][5][0:5] != 'SRP68':\n",
    "    #    continue\n",
    "    #print (f'qseqid, pdb_group = {qseqid}, {pdb_group}')\n",
    "    \n",
    "    if pdb_group[0][5] in appris_transcripts:\n",
    "        continue\n",
    "    # Get the top hit based on bitscore\n",
    "    # print (pdb_group)\n",
    "    #top_hit = max(pdb_group, key=lambda row:float(row[10]))\n",
    "    #print (f'top_hit = {top_hit}')\n",
    "    top_hit=[]\n",
    "    top_bitscore = 0.\n",
    "    for pg in pdb_group:\n",
    "        if float(pg[10]) > top_bitscore:\n",
    "            top_hit = pg\n",
    "            \n",
    "    top_bitscore = float(top_hit[10])\n",
    "    bitscore_threshold = top_bitscore * 0.9\n",
    "    \n",
    "    # Get all other hits with the same bitscore as the top hit\n",
    "    ## Note other_hits will now include all that match top_bitscore \n",
    "    hits = [row for row in pdb_group if float(row[10]) == top_bitscore]\n",
    "    second_tier = [row for row in pdb_group if bitscore_threshold < float(row[10]) < top_bitscore ]\n",
    "    \n",
    "    # Determine if all sseqids are nonappris-\n",
    "    all_nonappris = all(row[5] in nonappris_transcripts for row in hits)\n",
    "    \n",
    "    # If all sseqids are nonappris, add the gene name to each row and output to the filtered list\n",
    "    if all_nonappris:\n",
    "        gene_name = top_hit[5].split('-')[0]\n",
    "        #top_hit_with_gene = top_hit + [gene_name]\n",
    "        #filtered_pdb_to_gencode.append(top_hit_with_gene)\n",
    "        for hit in hits:\n",
    "            hit_with_gene = hit + [gene_name]\n",
    "            filtered_pdb_to_gencode.append(hit_with_gene)\n",
    "        for hit in second_tier:\n",
    "            if hit[5] in appris_transcripts:\n",
    "                genes_with_ref.add(gene_name)\n",
    "                also_refs[gene_name].add(hit[5] )\n",
    "                ref_pdbs[gene_name].append(hit[1] )\n",
    "    count += 1\n",
    "    if count == 3:\n",
    "        pass#break\n",
    "print (f'filtered_pdb_to_gencode is {len(filtered_pdb_to_gencode)} long')\n",
    "\n",
    "#print (filtered_pdb_to_gencode)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[['517',\n",
       "  '7e8h_I,K',\n",
       "  '760',\n",
       "  '24',\n",
       "  '119',\n",
       "  'DPP10-206',\n",
       "  '97',\n",
       "  '2',\n",
       "  '96',\n",
       "  '1.03e-22',\n",
       "  '94.7',\n",
       "  '96',\n",
       "  '43',\n",
       "  '1',\n",
       "  '1',\n",
       "  '52',\n",
       "  '44.792',\n",
       "  'DPP10'],\n",
       " ['842',\n",
       "  '2fy2_A',\n",
       "  '612',\n",
       "  '471',\n",
       "  '605',\n",
       "  'CRAT-217',\n",
       "  '551',\n",
       "  '422',\n",
       "  '547',\n",
       "  '6.30e-24',\n",
       "  '107',\n",
       "  '135',\n",
       "  '56',\n",
       "  '9',\n",
       "  '2',\n",
       "  '70',\n",
       "  '41.481',\n",
       "  'CHAT'],\n",
       " ['866',\n",
       "  '2fy2_A',\n",
       "  '612',\n",
       "  '262',\n",
       "  '309',\n",
       "  'CHAT-210',\n",
       "  '72',\n",
       "  '1',\n",
       "  '48',\n",
       "  '7.71e-28',\n",
       "  '107',\n",
       "  '48',\n",
       "  '48',\n",
       "  '0',\n",
       "  '0',\n",
       "  '0',\n",
       "  '100.000',\n",
       "  'CHAT'],\n",
       " ['949',\n",
       "  '6b0b_A,E',\n",
       "  '186',\n",
       "  '4',\n",
       "  '183',\n",
       "  'APOBEC3B-203',\n",
       "  '490',\n",
       "  '9',\n",
       "  '188',\n",
       "  '3.47e-21',\n",
       "  '91.3',\n",
       "  '187',\n",
       "  '59',\n",
       "  '14',\n",
       "  '4',\n",
       "  '114',\n",
       "  '31.551',\n",
       "  'APOBEC3B'],\n",
       " ['999',\n",
       "  '6vwb_A',\n",
       "  '90',\n",
       "  '37',\n",
       "  '90',\n",
       "  'MUS81-202',\n",
       "  '389',\n",
       "  '2',\n",
       "  '55',\n",
       "  '1.60e-30',\n",
       "  '112',\n",
       "  '54',\n",
       "  '54',\n",
       "  '0',\n",
       "  '0',\n",
       "  '0',\n",
       "  '100.000',\n",
       "  'MUS81'],\n",
       " ['1109',\n",
       "  '4kmn_A',\n",
       "  '103',\n",
       "  '4',\n",
       "  '43',\n",
       "  'BIRC2-205',\n",
       "  '262',\n",
       "  '220',\n",
       "  '259',\n",
       "  '4.88e-21',\n",
       "  '85.5',\n",
       "  '40',\n",
       "  '40',\n",
       "  '0',\n",
       "  '0',\n",
       "  '0',\n",
       "  '100.000',\n",
       "  'BIRC2'],\n",
       " ['1115',\n",
       "  '1deb_A,B',\n",
       "  '54',\n",
       "  '1',\n",
       "  '54',\n",
       "  'APC2-204',\n",
       "  '137',\n",
       "  '4',\n",
       "  '57',\n",
       "  '3.14e-21',\n",
       "  '80.9',\n",
       "  '54',\n",
       "  '38',\n",
       "  '0',\n",
       "  '0',\n",
       "  '16',\n",
       "  '70.370',\n",
       "  'APC2'],\n",
       " ['2268',\n",
       "  '3nru_A,B,C,D,E,F,G,H,I,J,K,L',\n",
       "  '187',\n",
       "  '3',\n",
       "  '102',\n",
       "  'EPHB6-207',\n",
       "  '183',\n",
       "  '33',\n",
       "  '136',\n",
       "  '1.16e-22',\n",
       "  '90.9',\n",
       "  '104',\n",
       "  '41',\n",
       "  '4',\n",
       "  '1',\n",
       "  '59',\n",
       "  '39.423',\n",
       "  'EPHB6'],\n",
       " ['2399',\n",
       "  '4afl_A,B,C,D,E,F',\n",
       "  '104',\n",
       "  '10',\n",
       "  '104',\n",
       "  'ING5-213',\n",
       "  '254',\n",
       "  '13',\n",
       "  '107',\n",
       "  '4.96e-44',\n",
       "  '144',\n",
       "  '95',\n",
       "  '69',\n",
       "  '0',\n",
       "  '0',\n",
       "  '26',\n",
       "  '72.632',\n",
       "  'ING5'],\n",
       " ['2642',\n",
       "  '5xhk_A',\n",
       "  '115',\n",
       "  '3',\n",
       "  '115',\n",
       "  'BRDT-211',\n",
       "  '238',\n",
       "  '25',\n",
       "  '135',\n",
       "  '2.11e-27',\n",
       "  '102',\n",
       "  '114',\n",
       "  '51',\n",
       "  '4',\n",
       "  '3',\n",
       "  '59',\n",
       "  '44.737',\n",
       "  'BRDT']]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_pdb_to_gencode[0:10]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Get some statistics"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "filtered_pdb_to_gencode is 8230 records long\n",
      "The reduced set of pdb_matches comprises 6249 PDBs that match 2077 genes.\n",
      "For these genes, 109 genes also have well-matched (bitscore >90% top bitscore) reference isoform (225 isoforms).\n"
     ]
    }
   ],
   "source": [
    "#print(filtered_pdb_to_gencode[0:3])\n",
    "print (f'filtered_pdb_to_gencode is {len(filtered_pdb_to_gencode)} records long')\n",
    "pdb_set= set()\n",
    "gene_set= set()\n",
    "for group in filtered_pdb_to_gencode:\n",
    "    pdb_set.add(group[1])\n",
    "    gene_set.add(group[17])\n",
    "num_pdb_refs = sum ([len (also_refs[gene]) for gene in also_refs])\n",
    "print (f'The reduced set of pdb_matches comprises {len(pdb_set)} PDBs that match {len (gene_set)} genes.')\n",
    "print (f'For these genes, {len(genes_with_ref)} genes also have well-matched (bitscore >90% top bitscore) reference isoform ({num_pdb_refs} isoforms).'  )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "just_alt = gene_set - genes_with_ref\n",
    "print (len(just_alt) )\n",
    "print (f'These have just_alt\\n{just_alt}')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "        text-align: right;\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>qseqid</th>\n",
       "      <th>qlen</th>\n",
       "      <th>qstart</th>\n",
       "      <th>qend</th>\n",
       "      <th>sseqid</th>\n",
       "      <th>slen</th>\n",
       "      <th>sstart</th>\n",
       "      <th>send</th>\n",
       "      <th>evalue</th>\n",
       "      <th>bitscore</th>\n",
       "      <th>length</th>\n",
       "      <th>nident</th>\n",
       "      <th>gaps</th>\n",
       "      <th>gapopen</th>\n",
       "      <th>mismatch</th>\n",
       "      <th>pident</th>\n",
       "      <th>gene</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>3745</th>\n",
       "      <td>5t5s_A</td>\n",
       "      <td>215</td>\n",
       "      <td>7</td>\n",
       "      <td>215</td>\n",
       "      <td>AARS1-203</td>\n",
       "      <td>999</td>\n",
       "      <td>757</td>\n",
       "      <td>996</td>\n",
       "      <td>7.13e-135</td>\n",
       "      <td>404</td>\n",
       "      <td>240</td>\n",
       "      <td>208</td>\n",
       "      <td>31</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>86.667</td>\n",
       "      <td>AARS1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5384</th>\n",
       "      <td>4xem_A</td>\n",
       "      <td>475</td>\n",
       "      <td>21</td>\n",
       "      <td>68</td>\n",
       "      <td>AARS1-235</td>\n",
       "      <td>48</td>\n",
       "      <td>1</td>\n",
       "      <td>48</td>\n",
       "      <td>1.30e-26</td>\n",
       "      <td>102</td>\n",
       "      <td>48</td>\n",
       "      <td>48</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>AARS1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5383</th>\n",
       "      <td>4xeo_A,B</td>\n",
       "      <td>475</td>\n",
       "      <td>21</td>\n",
       "      <td>68</td>\n",
       "      <td>AARS1-235</td>\n",
       "      <td>48</td>\n",
       "      <td>1</td>\n",
       "      <td>48</td>\n",
       "      <td>1.40e-26</td>\n",
       "      <td>102</td>\n",
       "      <td>48</td>\n",
       "      <td>48</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>AARS1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7937</th>\n",
       "      <td>5knn_A,B,C,D,E,F,G,H</td>\n",
       "      <td>450</td>\n",
       "      <td>1</td>\n",
       "      <td>45</td>\n",
       "      <td>AARS1-235</td>\n",
       "      <td>48</td>\n",
       "      <td>4</td>\n",
       "      <td>48</td>\n",
       "      <td>7.22e-25</td>\n",
       "      <td>97.8</td>\n",
       "      <td>45</td>\n",
       "      <td>45</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>AARS1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1741</th>\n",
       "      <td>6aam_A</td>\n",
       "      <td>298</td>\n",
       "      <td>6</td>\n",
       "      <td>211</td>\n",
       "      <td>AATK-202</td>\n",
       "      <td>879</td>\n",
       "      <td>118</td>\n",
       "      <td>331</td>\n",
       "      <td>4.60e-21</td>\n",
       "      <td>94.7</td>\n",
       "      <td>220</td>\n",
       "      <td>70</td>\n",
       "      <td>20</td>\n",
       "      <td>6</td>\n",
       "      <td>130</td>\n",
       "      <td>31.818</td>\n",
       "      <td>AATK</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1919</th>\n",
       "      <td>5kl6_A</td>\n",
       "      <td>93</td>\n",
       "      <td>6</td>\n",
       "      <td>91</td>\n",
       "      <td>ZNF544-215</td>\n",
       "      <td>573</td>\n",
       "      <td>459</td>\n",
       "      <td>540</td>\n",
       "      <td>8.45e-21</td>\n",
       "      <td>86.3</td>\n",
       "      <td>86</td>\n",
       "      <td>42</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>40</td>\n",
       "      <td>48.837</td>\n",
       "      <td>ZNF544</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3876</th>\n",
       "      <td>6vtx_A</td>\n",
       "      <td>84</td>\n",
       "      <td>8</td>\n",
       "      <td>83</td>\n",
       "      <td>ZNF544-215</td>\n",
       "      <td>573</td>\n",
       "      <td>439</td>\n",
       "      <td>512</td>\n",
       "      <td>7.86e-21</td>\n",
       "      <td>85.9</td>\n",
       "      <td>76</td>\n",
       "      <td>38</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>36</td>\n",
       "      <td>50.000</td>\n",
       "      <td>ZNF544</td>\n",
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       "    <tr>\n",
       "      <th>1918</th>\n",
       "      <td>4r2e_A</td>\n",
       "      <td>93</td>\n",
       "      <td>5</td>\n",
       "      <td>91</td>\n",
       "      <td>ZNF565-207</td>\n",
       "      <td>259</td>\n",
       "      <td>154</td>\n",
       "      <td>236</td>\n",
       "      <td>9.78e-21</td>\n",
       "      <td>84.0</td>\n",
       "      <td>87</td>\n",
       "      <td>42</td>\n",
       "      <td>4</td>\n",
       "      <td>2</td>\n",
       "      <td>41</td>\n",
       "      <td>48.276</td>\n",
       "      <td>ZNF565</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2071</th>\n",
       "      <td>7z36_D</td>\n",
       "      <td>70</td>\n",
       "      <td>1</td>\n",
       "      <td>68</td>\n",
       "      <td>ZNF607-203</td>\n",
       "      <td>102</td>\n",
       "      <td>4</td>\n",
       "      <td>71</td>\n",
       "      <td>8.18e-21</td>\n",
       "      <td>79.3</td>\n",
       "      <td>68</td>\n",
       "      <td>39</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>29</td>\n",
       "      <td>57.353</td>\n",
       "      <td>ZNF607</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3309</th>\n",
       "      <td>2dlk_A</td>\n",
       "      <td>79</td>\n",
       "      <td>8</td>\n",
       "      <td>64</td>\n",
       "      <td>ZNF692-213</td>\n",
       "      <td>79</td>\n",
       "      <td>9</td>\n",
       "      <td>65</td>\n",
       "      <td>1.15e-37</td>\n",
       "      <td>121</td>\n",
       "      <td>57</td>\n",
       "      <td>57</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>ZNF692</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>8230 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    qseqid qlen qstart qend      sseqid slen sstart send  \\\n",
       "3745                5t5s_A  215      7  215   AARS1-203  999    757  996   \n",
       "5384                4xem_A  475     21   68   AARS1-235   48      1   48   \n",
       "5383              4xeo_A,B  475     21   68   AARS1-235   48      1   48   \n",
       "7937  5knn_A,B,C,D,E,F,G,H  450      1   45   AARS1-235   48      4   48   \n",
       "1741                6aam_A  298      6  211    AATK-202  879    118  331   \n",
       "...                    ...  ...    ...  ...         ...  ...    ...  ...   \n",
       "1919                5kl6_A   93      6   91  ZNF544-215  573    459  540   \n",
       "3876                6vtx_A   84      8   83  ZNF544-215  573    439  512   \n",
       "1918                4r2e_A   93      5   91  ZNF565-207  259    154  236   \n",
       "2071                7z36_D   70      1   68  ZNF607-203  102      4   71   \n",
       "3309                2dlk_A   79      8   64  ZNF692-213   79      9   65   \n",
       "\n",
       "         evalue bitscore length nident gaps gapopen mismatch   pident    gene  \n",
       "3745  7.13e-135      404    240    208   31       1        1   86.667   AARS1  \n",
       "5384   1.30e-26      102     48     48    0       0        0  100.000   AARS1  \n",
       "5383   1.40e-26      102     48     48    0       0        0  100.000   AARS1  \n",
       "7937   7.22e-25     97.8     45     45    0       0        0  100.000   AARS1  \n",
       "1741   4.60e-21     94.7    220     70   20       6      130   31.818    AATK  \n",
       "...         ...      ...    ...    ...  ...     ...      ...      ...     ...  \n",
       "1919   8.45e-21     86.3     86     42    4       2       40   48.837  ZNF544  \n",
       "3876   7.86e-21     85.9     76     38    2       1       36   50.000  ZNF544  \n",
       "1918   9.78e-21     84.0     87     42    4       2       41   48.276  ZNF565  \n",
       "2071   8.18e-21     79.3     68     39    0       0       29   57.353  ZNF607  \n",
       "3309   1.15e-37      121     57     57    0       0        0  100.000  ZNF692  \n",
       "\n",
       "[8230 rows x 17 columns]"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined_filtered =  [sublist for sublist in filtered_pdb_to_gencode ]\n",
    "#print (combined_filtered)\n",
    "columns =  ['index','qseqid','qlen', 'qstart', 'qend', 'sseqid', 'slen', 'sstart', 'send', 'evalue', 'bitscore', 'length', 'nident', 'gaps','gapopen', 'mismatch', 'pident', 'gene']\n",
    "non_appris_pdbs =pd.DataFrame(combined_filtered, columns=columns)\n",
    "non_appris_pdbs =non_appris_pdbs.drop(columns=['index'])\n",
    "non_appris_pdbs = non_appris_pdbs.sort_values(by=['gene','sseqid','qseqid'])\n",
    "non_appris_pdbs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Function to extract sequences of Isoforms and related sequences\n",
    "USE: get_gene_seqs (gene, df=found_df)  \n",
    "By default, will extract data from found_df, but can be specified  \n",
    "##### default_df is currently non_appris_pdbs \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "default_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['FZD7-201', 'FZD1-201', 'PTGR2-201', 'PTGR2-204', 'FAU-203', 'FAU-205', 'MAPK1-202', 'MAPK1-201', 'DPP6-203', 'DPP6-201']\n"
     ]
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       "      <td>FZD7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>7evw_R</td>\n",
       "      <td>599.0</td>\n",
       "      <td>36.0</td>\n",
       "      <td>574.0</td>\n",
       "      <td>FZD1-201</td>\n",
       "      <td>647.0</td>\n",
       "      <td>103.0</td>\n",
       "      <td>647.0</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>905.0</td>\n",
       "      <td>551.0</td>\n",
       "      <td>440.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>93.0</td>\n",
       "      <td>79.855</td>\n",
       "      <td>FZD1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2zb4_A</td>\n",
       "      <td>357.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>357.0</td>\n",
       "      <td>PTGR2-201</td>\n",
       "      <td>351.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>351.0</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>728.0</td>\n",
       "      <td>351.0</td>\n",
       "      <td>351.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>PTGR2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2zb4_A</td>\n",
       "      <td>357.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>357.0</td>\n",
       "      <td>PTGR2-204</td>\n",
       "      <td>351.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>351.0</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>728.0</td>\n",
       "      <td>351.0</td>\n",
       "      <td>351.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>PTGR2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>7tql_e</td>\n",
       "      <td>51.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>FAU-203</td>\n",
       "      <td>98.0</td>\n",
       "      <td>44.0</td>\n",
       "      <td>98.0</td>\n",
       "      <td>1.560000e-23</td>\n",
       "      <td>85.5</td>\n",
       "      <td>55.0</td>\n",
       "      <td>46.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>83.636</td>\n",
       "      <td>FAU</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69093</th>\n",
       "      <td>4z0x_A</td>\n",
       "      <td>105.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>93.0</td>\n",
       "      <td>IGLV3-21-201</td>\n",
       "      <td>117.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>113.0</td>\n",
       "      <td>1.250000e-50</td>\n",
       "      <td>156.0</td>\n",
       "      <td>93.0</td>\n",
       "      <td>74.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>79.570</td>\n",
       "      <td>IGLV3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69094</th>\n",
       "      <td>2z9a_A,B</td>\n",
       "      <td>88.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>81.0</td>\n",
       "      <td>PSAP-201</td>\n",
       "      <td>524.0</td>\n",
       "      <td>311.0</td>\n",
       "      <td>389.0</td>\n",
       "      <td>7.630000e-47</td>\n",
       "      <td>157.0</td>\n",
       "      <td>79.0</td>\n",
       "      <td>79.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>PSAP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69095</th>\n",
       "      <td>2z9a_A,B</td>\n",
       "      <td>88.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>PSAP-204</td>\n",
       "      <td>167.0</td>\n",
       "      <td>115.0</td>\n",
       "      <td>167.0</td>\n",
       "      <td>4.070000e-31</td>\n",
       "      <td>108.0</td>\n",
       "      <td>53.0</td>\n",
       "      <td>53.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>PSAP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69096</th>\n",
       "      <td>8d58_A</td>\n",
       "      <td>246.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>246.0</td>\n",
       "      <td>METTL1-202</td>\n",
       "      <td>276.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>265.0</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>516.0</td>\n",
       "      <td>246.0</td>\n",
       "      <td>246.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>100.000</td>\n",
       "      <td>METTL1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69097</th>\n",
       "      <td>8d58_A</td>\n",
       "      <td>246.0</td>\n",
       "      <td>104.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>METTL1-204</td>\n",
       "      <td>124.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>124.0</td>\n",
       "      <td>3.650000e-85</td>\n",
       "      <td>250.0</td>\n",
       "      <td>137.0</td>\n",
       "      <td>123.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>89.781</td>\n",
       "      <td>METTL1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>69098 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         qseqid   qlen  qstart   qend        sseqid   slen  sstart   send  \\\n",
       "0        7evw_R  599.0    38.0  574.0      FZD7-201  574.0    38.0  574.0   \n",
       "1        7evw_R  599.0    36.0  574.0      FZD1-201  647.0   103.0  647.0   \n",
       "2        2zb4_A  357.0     7.0  357.0     PTGR2-201  351.0     1.0  351.0   \n",
       "3        2zb4_A  357.0     7.0  357.0     PTGR2-204  351.0     1.0  351.0   \n",
       "4        7tql_e   51.0     4.0   51.0       FAU-203   98.0    44.0   98.0   \n",
       "...         ...    ...     ...    ...           ...    ...     ...    ...   \n",
       "69093    4z0x_A  105.0     1.0   93.0  IGLV3-21-201  117.0    21.0  113.0   \n",
       "69094  2z9a_A,B   88.0     3.0   81.0      PSAP-201  524.0   311.0  389.0   \n",
       "69095  2z9a_A,B   88.0     3.0   55.0      PSAP-204  167.0   115.0  167.0   \n",
       "69096    8d58_A  246.0     1.0  246.0    METTL1-202  276.0    20.0  265.0   \n",
       "69097    8d58_A  246.0   104.0  240.0    METTL1-204  124.0     2.0  124.0   \n",
       "\n",
       "             evalue  bitscore  length  nident  gaps  gapopen  mismatch  \\\n",
       "0      0.000000e+00    1115.0   537.0   537.0   0.0      0.0       0.0   \n",
       "1      0.000000e+00     905.0   551.0   440.0  18.0      6.0      93.0   \n",
       "2      0.000000e+00     728.0   351.0   351.0   0.0      0.0       0.0   \n",
       "3      0.000000e+00     728.0   351.0   351.0   0.0      0.0       0.0   \n",
       "4      1.560000e-23      85.5    55.0    46.0   7.0      1.0       2.0   \n",
       "...             ...       ...     ...     ...   ...      ...       ...   \n",
       "69093  1.250000e-50     156.0    93.0    74.0   0.0      0.0      19.0   \n",
       "69094  7.630000e-47     157.0    79.0    79.0   0.0      0.0       0.0   \n",
       "69095  4.070000e-31     108.0    53.0    53.0   0.0      0.0       0.0   \n",
       "69096  0.000000e+00     516.0   246.0   246.0   0.0      0.0       0.0   \n",
       "69097  3.650000e-85     250.0   137.0   123.0  14.0      1.0       0.0   \n",
       "\n",
       "        pident    gene  \n",
       "0      100.000    FZD7  \n",
       "1       79.855    FZD1  \n",
       "2      100.000   PTGR2  \n",
       "3      100.000   PTGR2  \n",
       "4       83.636     FAU  \n",
       "...        ...     ...  \n",
       "69093   79.570   IGLV3  \n",
       "69094  100.000    PSAP  \n",
       "69095  100.000    PSAP  \n",
       "69096  100.000  METTL1  \n",
       "69097   89.781  METTL1  \n",
       "\n",
       "[69098 rows x 17 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df4 = pd.read_csv('Data/top2_pdb_vs_gencode.tsv', sep='\\t')\n",
    "df4 = df4.drop(columns =['Unnamed: 0'])\n",
    "#df4['sseqid'] = [s.split('|')[0] for s in df4['sseqid'].to_list()]\n",
    "my_list = []\n",
    "for s in df4['sseqid'].to_list():\n",
    "    my_list.append (str(s).split('|')[0])\n",
    "print (my_list[0:10])\n",
    "df4['sseqid']= my_list\n",
    "df4['gene']= [s.split('-')[0] for s in df4['sseqid'].to_list()]\n",
    "df4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(['CD44-206'], ['CD44-201', 'CD44-202', 'CD44-203', 'CD44-204', 'CD44-205', 'CD44-207', 'CD44-208', 'CD44-209', 'CD44-210', 'CD44-211', 'CD44-212', 'CD44-213', 'CD44-214', 'CD44-215', 'CD44-216', 'CD44-217', 'CD44-218', 'CD44-219', 'CD44-220', 'CD44-221', 'CD44-222', 'CD44-223', 'CD44-224', 'CD44-225', 'CD44-226', 'CD44-227', 'CD44-228', 'CD44-229', 'CD44-230', 'CD44-231', 'CD44-232', 'CD44-233', 'CD44-234', 'CD44-235', 'CD44-236', 'CD44-237', 'CD44-238'])\n"
     ]
    }
   ],
   "source": [
    "print (ref_nonref('CD44'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "[s.split('|')[0] for s in df4['sseqid']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['>4wyq_B,E', 'ALGPACCRVLSELSEEQAFHVSYLDIEELSLSGLCQCLVELSTQPATVCHGSATTREAARGEAARRALQYLKIMA', '>6zbk_B']\n"
     ]
    }
   ],
   "source": [
    "pdb_file='Data/pdb_unique_human_seqs_230301.fa'\n",
    "gene_file='Data/gencode_v43_translations_mod.fa'\n",
    "default_df = df4\n",
    "def extract_sequence(filename, sequence_id):\n",
    "    sequence = \"\"\n",
    "    with open(filename, \"r\") as f:\n",
    "        for line in f:\n",
    "            if line.startswith(\">\") and sequence_id in line:\n",
    "                if '|' in line:\n",
    "                    sequence += line.split('|')[0] + '\\n'\n",
    "                else:\n",
    "                     sequence += line\n",
    "                # Found the sequence ID we want\n",
    "                while True:\n",
    "                    line = f.readline().strip()\n",
    "                    if line.startswith(\">\") or not line:\n",
    "                        # Reached the end of the sequence\n",
    "                        break\n",
    "                    sequence += line\n",
    "    sequence += \"\\n\"\n",
    "    return sequence\n",
    "def get_gene_seqs (gene, df=default_df, field='sseqid'):\n",
    "    matches = df.loc[ df[field].str.contains(gene) ]\n",
    "    isos = set()\n",
    "    pdbs = set()\n",
    "    for i,row in matches.iterrows():\n",
    "        isos.add(row['sseqid'])\n",
    "        pdbs.add(row['qseqid'])\n",
    "    seqs=\"\"\n",
    "    for pdb in pdbs:\n",
    "        seqs+= extract_sequence (pdb_file, pdb)\n",
    "    for iso in isos:\n",
    "        seqs+= extract_sequence (gene_file, iso)\n",
    "    return (seqs)\n",
    "def get_all_gene_seq(gene):\n",
    "    ref,nonref = ref_nonref(gene)\n",
    "def pdbs_with_appris (gene, df=default_df):\n",
    "    matches = df.loc[ df['sseqid'].str.contains(gene) ]\n",
    "    pdbs = set()\n",
    "    genes = set()\n",
    "    isos = set()\n",
    "    for i,row in matches.iterrows():\n",
    "        pdbs.add(row['qseqid'])\n",
    "        genes.add(row['gene'])\n",
    "        isos.add(row['sseqid'])\n",
    "    #print (pdbs, genes)\n",
    "    seqs=\"\"\n",
    "    for pdb in pdbs:\n",
    "        seqs+= extract_sequence (pdb_file, pdb)\n",
    "    for gene in genes:\n",
    "        to_get, dont_get = ref_nonref(gene)\n",
    "        if to_get:\n",
    "            seqs += extract_sequence (gene_file, to_get[0]).replace('>','>REF_')\n",
    "    for iso in isos:\n",
    "        seqs+= extract_sequence (gene_file, iso).replace('>','>ALT_')\n",
    "        \n",
    "        #if gene in genes_with_ref:\n",
    "        #    for iso in also_refs[gene]:\n",
    "        #        seqs += extract_sequence(gene_file, iso).replace('>','>REF_')\n",
    "        #    for pdb in ref_pdbs[gene]:\n",
    "        #        seqs += extract_sequence(pdb_file, pdb).replace('>','>REF_')\n",
    "    return (seqs)\n",
    "\n",
    "\n",
    "\n",
    "s=pdbs_with_appris('TARBP2')\n",
    "print (s.splitlines()[0:3])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">ref_CD44-206\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATSTSSNTISAGWEPNEENEDERDRHLSFSGSGIDDDEDFISSTISTTPRAFDHTKQNQDWTQWNPSHSNPEVLLQTTTRMTDVDRNGTTAYEGNWNPEAHPPLIHHEHHEEEETPHSTSTIQATPSSTTEETATQKEQWFGNRWHEGYRQTPKEDSHSTTGTAAASAHTSHPMQGRTTPSPEDSSWTDFFNPISHPMGRGHQAGRRMDMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRNDVTGGRRDPNHSEGSTTLLEGYTSHYPHTKESRTFIPVTSAKTGSFGVTAVTVGDSNSNVNRSLSGDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      ">alt_CD44-201\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATRDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      ">alt_CD44-202\n",
      "PEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATNMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSRDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLV\n",
      ">alt_CD44-203\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCSLHCSQQSKKVWAEEKASDQQWQWSCGGQKAKWTQRRGQQVSGNGAFGEQGVVRNSRPVYDS\n",
      ">alt_CD44-204\n",
      "RYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMK\n",
      ">alt_CD44-205\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATRHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      ">alt_CD44-207\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCSST\n",
      ">alt_CD44-208\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATTLMSTSATATETATKRQETWDWFSWLFLPSESKNHLHTTTQMAGTSSNTISAGWEPNEENEDERDRHLSFSGSGIDDDEDFISSTISTTPRAFDHTKQNQDWTQWNPSHSNPEVLLQTTTRMTDVDRNGTTAYEGNWNPEAHPPLIHHEHHEEEETPHSTSTIQATPSSTTEETATQKEQWFGNRWHEGYRQTPKEDSHSTTGTAAASAHTSHPMQGRTTPSPEDSSWTDFFNPISHPMGRGHQAGRRMDMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRNDVTGGRRDPNHSEGSTTLLEGYTSHYPHTKESRTFIPVTSAKTGSFGVTAVTVGDSNSNVNRSLSGDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      ">alt_CD44-209\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATNMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRNDVTGGRRDPNHSEGSTTLLEGYTSHYPHTKESRTFIPVTSAKTGSFGVTAVTVGDSNSNVNRSLSGDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      ">alt_CD44-210\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATNRNDVTGGRRDPNHSEGSTTLLEGYTSHYPHTKESRTFIPVTSAKTGSFGVTAVTVGDSNSNVNRSLSGDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      ">alt_CD44-211\n",
      "XDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATRDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRS\n",
      ">alt_CD44-212\n",
      "XPDEDSPWITDSTDRIPATSWEPNEENEDERDRHLSFSGSGIDDDEDFISSTISTTPRAFDHTKQNQDWTQWNPSHSNPEVLLQTTTRMTDVDRNGTTAYEGNWNPEAHPPLIHHEHH\n",
      "\n",
      ">alt_CD44-214\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATTASAHTSHPMQGRTTPSPEDSSWTDFFNPISHPMGRGHQAGRRMDMDSSHSITLQ\n",
      "\n",
      "\n",
      "\n",
      ">alt_CD44-218\n",
      "SKHNLWSYKDTPNSRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      ">alt_CD44-219\n",
      "XDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATTLMSTSATATETATKRQETWDWFSWLFLPSESKNHLHTTTQMAGTSSNTISAGWEPNEENEDERDRHLSFSGSGIDDDEDFISSTNMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRND\n",
      ">alt_CD44-220\n",
      "RTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATSTSSNTISAGWEPNEENEDERDRHLSFSGSGIDDDEDFISSTRDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINS\n",
      ">alt_CD44-221\n",
      "XLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGDRNDVTGGRRDPNHSEGSTTLLEGYTSHYPHTKESRTFIPVTSAKTGSFGVTAVTVGDSNSNVNRSLSGDQ\n",
      ">alt_CD44-222\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCR\n",
      ">alt_CD44-223\n",
      "XSTTPRAFDHTKQNQDWTQWNPSHSNPEVLLQTTTRMTVQATPSSTTEETATQKEQWFGNRWHEGYRQTPKEDSHSTTGTAASAHTSHPMQGRTTPSPEDSSWTDFFNPISHPMGRGHQAGRRMDMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRN\n",
      ">alt_CD44-224\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      "\n",
      ">alt_CD44-226\n",
      "XRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGDMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQ\n",
      "\n",
      ">alt_CD44-228\n",
      "XQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATISTTPRAFDHTKQNQDWTQWNPSHSNPEVLLQTTTRMTDVDRNGTTAYEGNWNPEAHPPLIHHEHHEEEE\n",
      ">alt_CD44-229\n",
      "RNGTTAYEGNWNPEAHPPLIHHEHHEEEETPHSTSTIQATPSSTTEETATQKEQWFGNRWHEGYRQTPKEDSHSTTGTADMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRNDVTGGRRDPNHSEGSTTLLEGYTSHYPHTKESRTFIPVTSAKTGSFGVT\n",
      "\n",
      ">alt_CD44-231\n",
      "EDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATIQATPSSTTEETATQKEQWFGNRWHEGYRQTPKEDSHSTTGTAAASAHTSHPMQGRTTPSPEDSSWTDFFNPISHPMGRGHQAGRRMDMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRNDVTGGRRDPNHSEGSTTL\n",
      "\n",
      "\n",
      ">alt_CD44-234\n",
      "XFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATKQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRNDVTGGRRDPNHSEGSTTLL\n",
      "\n",
      ">alt_CD44-236\n",
      "IYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATSTSSNTISAGWEPNEENEDERDRHLSFSGSGIDDDEDFISSTNMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRNDVTGGRRDPNHSEGSTTLLEGYTSHYPHT\n",
      "\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "def get_all_gene_seqs(gene):\n",
    "    ref,nonref = ref_nonref(gene)\n",
    "    to_return = \"\"\n",
    "    for r in ref:\n",
    "        r_seq =  extract_sequence(gene_file,r).replace('>',\">ref_\")\n",
    "        to_return += r_seq\n",
    "    for n in nonref:\n",
    "        n_seq = extract_sequence(gene_file,n).replace('>',\">alt_\")\n",
    "        to_return += n_seq\n",
    "    return to_return\n",
    "print (get_all_gene_seqs('CD44'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#mrnr_df\n",
    "pdbs_with_appris('DCX',df4)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Publications\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pdbid</th>\n",
       "      <th>pdb_id</th>\n",
       "      <th>title</th>\n",
       "      <th>year</th>\n",
       "      <th>pmid</th>\n",
       "      <th>doi</th>\n",
       "      <th>journal_abbrev</th>\n",
       "      <th>volume</th>\n",
       "      <th>pages</th>\n",
       "      <th>journal_issn</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1wlp</td>\n",
       "      <td>1WLP</td>\n",
       "      <td>NMR solution structure of the tandem Src homol...</td>\n",
       "      <td>2006.0</td>\n",
       "      <td>16326715.0</td>\n",
       "      <td>10.1074/jbc.M505193200</td>\n",
       "      <td>J.Biol.Chem.</td>\n",
       "      <td>281</td>\n",
       "      <td>3660-3668</td>\n",
       "      <td>0021-9258</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1wo4</td>\n",
       "      <td>1WO4</td>\n",
       "      <td>Assessment of the robustness of a serendipitou...</td>\n",
       "      <td>2005.0</td>\n",
       "      <td>15698569.0</td>\n",
       "      <td>10.1016/j.str.2004.12.007</td>\n",
       "      <td>Structure</td>\n",
       "      <td>13</td>\n",
       "      <td>257-266</td>\n",
       "      <td>0969-2126</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1wso</td>\n",
       "      <td>1WSO</td>\n",
       "      <td>Orexin-A is composed of a highly conserved C-t...</td>\n",
       "      <td>2006.0</td>\n",
       "      <td>16429482.0</td>\n",
       "      <td>10.1002/psc.747</td>\n",
       "      <td>J.Pept.Sci.</td>\n",
       "      <td>12</td>\n",
       "      <td>443-454</td>\n",
       "      <td>1075-2617</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1wtg</td>\n",
       "      <td>1WTG</td>\n",
       "      <td>Novel interactions of large P3 moiety and smal...</td>\n",
       "      <td>2005.0</td>\n",
       "      <td>15607748.0</td>\n",
       "      <td>10.1016/j.bbrc.2004.11.108</td>\n",
       "      <td>Biochem.Biophys.Res.Commun.</td>\n",
       "      <td>326</td>\n",
       "      <td>859-865</td>\n",
       "      <td>0006-291X</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1wvo</td>\n",
       "      <td>1WVO</td>\n",
       "      <td>Solution structure of the antifreeze-like doma...</td>\n",
       "      <td>2006.0</td>\n",
       "      <td>16597820.0</td>\n",
       "      <td>10.1110/ps.051700406</td>\n",
       "      <td>Protein Sci.</td>\n",
       "      <td>15</td>\n",
       "      <td>1010-1016</td>\n",
       "      <td>0961-8368</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52982</th>\n",
       "      <td>1wug</td>\n",
       "      <td>1WUG</td>\n",
       "      <td>Selective small molecules blocking HIV-1 Tat a...</td>\n",
       "      <td>2005.0</td>\n",
       "      <td>15724976.0</td>\n",
       "      <td>10.1021/ja044885g</td>\n",
       "      <td>J.Am.Chem.Soc.</td>\n",
       "      <td>127</td>\n",
       "      <td>2376-2377</td>\n",
       "      <td>0002-7863</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52983</th>\n",
       "      <td>1wum</td>\n",
       "      <td>1WUM</td>\n",
       "      <td>Selective small molecules blocking HIV-1 Tat a...</td>\n",
       "      <td>2005.0</td>\n",
       "      <td>15724976.0</td>\n",
       "      <td>10.1021/ja044885g</td>\n",
       "      <td>J.Am.Chem.Soc.</td>\n",
       "      <td>127</td>\n",
       "      <td>2376-2377</td>\n",
       "      <td>0002-7863</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52984</th>\n",
       "      <td>1wuu</td>\n",
       "      <td>1WUU</td>\n",
       "      <td>Molecular Structure of Human Galactokinase: IM...</td>\n",
       "      <td>2005.0</td>\n",
       "      <td>15590630.0</td>\n",
       "      <td>10.1074/jbc.M412916200</td>\n",
       "      <td>J.Biol.Chem.</td>\n",
       "      <td>280</td>\n",
       "      <td>9662-9670</td>\n",
       "      <td>0021-9258</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52985</th>\n",
       "      <td>1wou</td>\n",
       "      <td>1WOU</td>\n",
       "      <td>Structural basis of cellular redox regulation ...</td>\n",
       "      <td>2004.0</td>\n",
       "      <td>15355959.0</td>\n",
       "      <td>10.1074/jbc.M407079200</td>\n",
       "      <td>J.Biol.Chem.</td>\n",
       "      <td>279</td>\n",
       "      <td>48120-48125</td>\n",
       "      <td>0021-9258</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52986</th>\n",
       "      <td>1wrm</td>\n",
       "      <td>1WRM</td>\n",
       "      <td>Crystal structure of human dual specificity ph...</td>\n",
       "      <td>2006.0</td>\n",
       "      <td>17068812.0</td>\n",
       "      <td>10.1002/prot.21152</td>\n",
       "      <td>Proteins</td>\n",
       "      <td>66</td>\n",
       "      <td>272-278</td>\n",
       "      <td>0887-3585</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>52987 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      pdbid pdb_id                                              title    year  \\\n",
       "0      1wlp   1WLP  NMR solution structure of the tandem Src homol...  2006.0   \n",
       "1      1wo4   1WO4  Assessment of the robustness of a serendipitou...  2005.0   \n",
       "2      1wso   1WSO  Orexin-A is composed of a highly conserved C-t...  2006.0   \n",
       "3      1wtg   1WTG  Novel interactions of large P3 moiety and smal...  2005.0   \n",
       "4      1wvo   1WVO  Solution structure of the antifreeze-like doma...  2006.0   \n",
       "...     ...    ...                                                ...     ...   \n",
       "52982  1wug   1WUG  Selective small molecules blocking HIV-1 Tat a...  2005.0   \n",
       "52983  1wum   1WUM  Selective small molecules blocking HIV-1 Tat a...  2005.0   \n",
       "52984  1wuu   1WUU  Molecular Structure of Human Galactokinase: IM...  2005.0   \n",
       "52985  1wou   1WOU  Structural basis of cellular redox regulation ...  2004.0   \n",
       "52986  1wrm   1WRM  Crystal structure of human dual specificity ph...  2006.0   \n",
       "\n",
       "             pmid                         doi               journal_abbrev  \\\n",
       "0      16326715.0      10.1074/jbc.M505193200                 J.Biol.Chem.   \n",
       "1      15698569.0   10.1016/j.str.2004.12.007                    Structure   \n",
       "2      16429482.0             10.1002/psc.747                  J.Pept.Sci.   \n",
       "3      15607748.0  10.1016/j.bbrc.2004.11.108  Biochem.Biophys.Res.Commun.   \n",
       "4      16597820.0        10.1110/ps.051700406                 Protein Sci.   \n",
       "...           ...                         ...                          ...   \n",
       "52982  15724976.0           10.1021/ja044885g               J.Am.Chem.Soc.   \n",
       "52983  15724976.0           10.1021/ja044885g               J.Am.Chem.Soc.   \n",
       "52984  15590630.0      10.1074/jbc.M412916200                 J.Biol.Chem.   \n",
       "52985  15355959.0      10.1074/jbc.M407079200                 J.Biol.Chem.   \n",
       "52986  17068812.0          10.1002/prot.21152                     Proteins   \n",
       "\n",
       "      volume        pages journal_issn  \n",
       "0        281    3660-3668    0021-9258  \n",
       "1         13      257-266    0969-2126  \n",
       "2         12      443-454    1075-2617  \n",
       "3        326      859-865    0006-291X  \n",
       "4         15    1010-1016    0961-8368  \n",
       "...      ...          ...          ...  \n",
       "52982    127    2376-2377    0002-7863  \n",
       "52983    127    2376-2377    0002-7863  \n",
       "52984    280    9662-9670    0021-9258  \n",
       "52985    279  48120-48125    0021-9258  \n",
       "52986     66      272-278    0887-3585  \n",
       "\n",
       "[52987 rows x 10 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "publications = pd.read_csv('Data/pdb_publications.tsv', sep = '\\t' )\n",
    "publications"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "if '4lsd' in publications['pdbid']:\n",
    "    print ('published')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'just_alt' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[25], line 5\u001b[0m\n\u001b[1;32m      3\u001b[0m pubs \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m      4\u001b[0m unpublished \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mset\u001b[39m()\n\u001b[0;32m----> 5\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m gene \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mlist\u001b[39m(\u001b[43mjust_alt\u001b[49m):\n\u001b[1;32m      6\u001b[0m     published \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0\u001b[39m \n\u001b[1;32m      7\u001b[0m     \u001b[38;5;66;03m#print (gene)\u001b[39;00m\n",
      "\u001b[0;31mNameError\u001b[0m: name 'just_alt' is not defined"
     ]
    }
   ],
   "source": [
    "#for just_alt, get pdbs and return t/f if in publications\n",
    "pdb_list = []\n",
    "pubs = []\n",
    "unpublished = set()\n",
    "for gene in list(just_alt):\n",
    "    published = 0 \n",
    "    #print (gene)\n",
    "    pdbs_for_genes_df = non_appris_pdbs[ non_appris_pdbs['sseqid'].str.startswith(gene)]\n",
    "    #print (f'{len(pdbs_for_genes_df)} pdbs')\n",
    "    for pdb in pdbs_for_genes_df['qseqid']:\n",
    "        #print (pdb, end =\"\")\n",
    "        if pdb[0:4] in publications['pdbid'].to_list():\n",
    "            published = 1\n",
    "            #print (f' published')\n",
    "        #else:\n",
    "            #print (' unpublished')\n",
    "    #print()\n",
    "    #print (f'pdb_list for {gene} is {pdb_list}')\n",
    "    if published == 0:\n",
    "        unpublished.add(gene)\n",
    "#pdbs_for_genes_df\n",
    "#pdbs_for_genes_df = non_appris_pdbs[ non_appris_pdbs['sseqid'].str.startswith('DCD')]\n",
    "print (f'unpublished list is {unpublished}')\n",
    "#print (pdb_list)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## MSA "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "#data_dir = 'Data/Non_appris_seqs'\n",
    "data_dir= 'Data/Seq_groups'\n",
    "#data_dir='Data/Aln_files'\n",
    "def one_msa(g):\n",
    "    fasta_file = f'{data_dir}/{g}.fa'\n",
    "    if not os.path.isfile(fasta_file):\n",
    "        s=get_gene_seqs(g)\n",
    "        with open (fasta_file, 'w') as out:\n",
    "            out.write(s)\n",
    "    msa_file = f'{data_dir}/{g}.aln'\n",
    "    if not os.path.isfile(msa_file):\n",
    "        cmd = f'clustalo -i {fasta_file} --outfmt=clu -o {msa_file}'\n",
    "        print (cmd)\n",
    "        r=subprocess.getoutput(cmd)\n",
    "        if r[0:5] ==\"ERROR\":\n",
    "            return (f'Something went wrong with {g}')\n",
    "        print (r)\n",
    "    with open (msa_file, 'r') as f:\n",
    "        rr=f.read()\n",
    "        print (rr)    \n",
    "    \n",
    "def show_msa(gene_list, fresh=0, last=None):\n",
    "    '''Will generate and show a MSA for a list of genes. If last is set, it will skip until it reaches that gene'''\n",
    "    if len(gene_list)==1:\n",
    "        fresh =1\n",
    "    for g in gene_list:\n",
    "        if fresh==0 and g!=last:\n",
    "            continue\n",
    "        print (g)\n",
    "        print (f'Reference isoform is {ref_nonref(g)[0]}')\n",
    "        fresh=1\n",
    "        last = g\n",
    "        fasta_file = f'{data_dir}/{g}.fa'\n",
    "        if not os.path.isfile(fasta_file):\n",
    "            s=get_gene_seqs(g)\n",
    "            with open (fasta_file, 'w') as out:\n",
    "                out.write(s)\n",
    "        msa_file = f'{data_dir}/{g}.aln'\n",
    "        if not os.path.isfile(msa_file):\n",
    "            cmd = f'clustalo -i {fasta_file} --outfmt=clu -o {msa_file}'\n",
    "            print (cmd)\n",
    "            r=subprocess.getoutput(cmd)\n",
    "            if r[0:5] ==\"ERROR\":\n",
    "                print (f'Something went wrong with {g}')\n",
    "                continue\n",
    "            print (r)\n",
    "        with open (msa_file, 'r') as f:\n",
    "            rr=f.read()\n",
    "            print (rr)\n",
    "\n",
    "        #read = input (\"Ready to move on? f to see sequence file \")\n",
    "        #if read.lower() == 'f':\n",
    "            with open (fastafile) as seqs:\n",
    "                print (seqs.read())\n",
    "            if len (gene_list) > 1:\n",
    "                read = input (\"Ready to move on? \")\n",
    "            \n",
    "def show_seqs_loop(gene_list, fresh=0, last=None):\n",
    "    #expects a df with the name of the gene in position 0\n",
    "    for g in gene_list:\n",
    "        #print (g)\n",
    "        if fresh==0 and g!=last:\n",
    "            continue\n",
    "        fresh=1\n",
    "        last = g   \n",
    "        with open (f'Data/Seq_groups/{g}.fa') as seqs:\n",
    "            print(seqs.read())\n",
    "        read = input (\"Ready to move on? f to see sequence file\")\n",
    "\n",
    "def show_seqs(gene):\n",
    "    with open (f'Data/Seq_groups/{gene}.fa') as seqs:\n",
    "        print (seqs.read())\n",
    "\n",
    "def matches_for_gene(gene, df = default_df):\n",
    "    df2 = df.loc[df['sseqid'].str.startswith(gene)]\n",
    "    return (df2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ">1poz_A\n",
      "AQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDV\n",
      ">4pz3_A,B\n",
      "AMAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYP\n",
      ">4pz4_A,B\n",
      "AMAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPS\n",
      ">2i83_A\n",
      "MAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDV\n",
      ">CD44-211|ENST00000442151.6\n",
      "XDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATRDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRS\n",
      ">CD44-214|ENST00000525211.6\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATTASAHTSHPMQGRTTPSPEDSSWTDFFNPISHPMGRGHQAGRRMDMDSSHSITLQ\n",
      ">CD44-205|ENST00000352818.8\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATRHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      "\n"
     ]
    }
   ],
   "source": [
    "show_seqs('CD44')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "matches_for_gene('IL1RAP')  #\n",
    "#matches_for_gene('AFF4', df=blast_df)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create a directory with sequence files for all the matches"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "failed = []\n",
    "dir = 'Data/Non_appris_seqs'\n",
    "for gene in set (non_appris_pdbs['gene'].tolist()):\n",
    "    file = f'{dir}/{gene}.fa'\n",
    "    if os.path.isfile(file):\n",
    "        continue\n",
    "    try:\n",
    "        s = pdbs_with_appris(gene)\n",
    "    except:\n",
    "        print (f'Something went wrong with {gene}')\n",
    "        failed.append(gene)\n",
    "    with open (file, 'w') as out:\n",
    "        out.write(s)\n",
    "if failed:\n",
    "    print (\"!!!!   !!!! Some things failed. Writen to failed_files.txt\")\n",
    "    with open (f'{dir}/failed_files.txt', 'w') as failed:\n",
    "       failed.write(failed)\n",
    "           \n",
    "print ('Done')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'TTN', 'CUTA', 'AFF4', 'SNAP25', 'SF3B4', 'ARID1A', 'ATP6V1H', 'VEGFA', 'PDE5A', 'NRP2', 'SLC12A6', 'SMARCA2', 'PDE4D', 'DMPK', 'KAT6A', 'ECT2', 'KCNN4', 'CR2', 'API5', 'RANBP3', 'NFYC', 'FGFR1', 'OTUD5', 'TFPI', 'PTK2', 'ANK1', 'ABCG1', 'PSMC3', 'CSF2RB', 'GOLGA2', 'PIK3R1', 'FGFR3', 'FXYD2', 'SPAST', 'HNRNPA2B1', 'ATP2A2', 'MAPK8', 'SEH1L', 'CERT1', 'MAT2B', 'ENAH', 'NTRK3', 'UBE2V1', 'AP1S3', 'ATP13A2', 'GABRG2', 'CAMK2G', 'CCR2', 'IGHM', 'NT5M', 'SULT2B1', 'AGAP3', 'BTRC', 'RICTOR', 'RAC1', 'BRD4', 'SIRPB1', 'BRD9', 'RAB11FIP3', 'LGALS9', 'RGS7', 'MGAM', 'NELFCD', 'TMPRSS13', 'DUSP13', 'ZFP64', 'NASP', 'CSF3', 'SLC12A5', 'GOLGA4', 'EZH2', 'PTEN', 'PXN', 'FN1', 'MCM3', 'MED16', 'CASP8', 'MACF1', 'GABRB3', 'MGLL', 'LRP8', 'PGM1', 'GIGYF2', 'ACLY', 'TRRAP', 'KDM1A', 'ADCYAP1R1', 'VPS29', 'GCK', 'CSF1', 'IMPDH1', 'PPFIA2', 'PAK6', 'NEDD4', 'GSN', 'ITGB1', 'DNM1', 'TRIO', 'PTCH1', 'DNMT3B', 'HNRNPK', 'VAV1', 'GRIA2', 'TUBGCP2', 'PSMA1', 'KCND3', 'DDR1', 'IL1RAP', 'PI4KB', 'INS', 'GNAS', 'SMARCB1', 'DNM1L', 'PTPN13', 'KIT', 'SLC3A2', 'BLM', 'CR1', 'BPTF', 'PCDH15', 'STK24', 'IKBKG', 'ISCU', 'GHRHR', 'KHK', 'PBRM1', 'TREX1', 'MRPS34', 'DYSF', 'ATL3', 'SLC9A3R1', 'PAK4', 'VASP', 'INSR', 'GSPT1', 'FGFR2', 'ACP3', 'PFKFB3', 'CAMK2D', 'TRIM33', 'MASP1', 'KCNIP1', 'CLPB', 'RARG', 'TJP1', 'AKAP7', 'CARD8', 'HARS1', 'GABBR1', 'IGF1', 'MACROH2A1', 'CREBBP', 'DPP6', 'MCU', 'PRKACA', 'USP2', 'GYPA', 'BRD2', 'YAP1', 'H2AZ2', 'GSDMB', 'MTA1', 'SPHK1', 'KRAS', 'SNUPN', 'SCN5A', 'ERAP1', 'MRPL43', 'ATP11C', 'ASB9', 'EXOSC9', 'UMOD', 'HDAC6', 'SEPTIN3', 'BAG6', 'USP28', 'PLEC', 'FMR1', 'SMARCA4', 'FERMT3', 'SMARCC2', 'CABP1', 'HGS', 'MOCS2', 'FGF13', 'LAMTOR5', 'ANK2', 'PTH1R', 'RHOT1', 'FZR1', 'PANK1', 'PBX1', 'SPINT1', 'MRPL22', 'CTNS', 'HNRNPD', 'CBFB', 'ISY1', 'MED15', 'RPS6KA1', 'CNOT6L', 'ABI2', 'CNGA3', 'CASK', 'NUDT1', 'PSMC6', 'AGER', 'BSG', 'NUMA1', 'DLG3', 'PRKG1', 'MED25', 'PRKAR2A', 'NEO1', 'SHANK3', 'RIMS2', 'VCL', 'UPF1', 'MAPT', 'SUPT20H', 'CHKA', 'KCNQ2', 'TNC', 'MAP3K3', 'TP73', 'CLIP1', 'CSNK1D', 'SNRPB', 'GYG1', 'GLS', 'KARS1', 'FLNB', 'PACSIN2', 'STRN3', 'TAF1', 'STAG2', 'GRIN1', 'NF1', 'NRG1', 'ACTN1', 'TRIM28', 'BRD3', 'IPO5', 'NUP98', 'STAT3', 'TARBP2', 'ACP1', 'PKM', 'SF1'}\n"
     ]
    }
   ],
   "source": [
    "just_nonref = set (pdb_nonref_list_by_gene)\n",
    "has_both = set (pdb_nonref_list_by_gene).intersection(set(pdb_ref_list_by_gene))\n",
    "print (has_both)\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NO AF2 Models found\n",
      "0\n"
     ]
    }
   ],
   "source": [
    "def get_af2s(gene):\n",
    "    to_return = []\n",
    "    ref,nonref = ref_nonref(gene)\n",
    "    #df = blast_df.loc[ blast_df['qseqid'].isin(pdb_nonref_list_by_gene[gene])]\n",
    "    df = blast_df.loc[ blast_df['qseqid'].isin(nonref)]\n",
    "    df2 = df.loc[df.groupby('qseqid')['bitscore'].idxmax()]\n",
    "    af2_ids = df2['sseqid'].map(gene_hash).unique()\n",
    "    if len(af2_ids) > 0:\n",
    "        for id in af2_ids:\n",
    "            if id in chess_dict:\n",
    "                file=f'{chess_pdb_dir}/{chess_dict[id]}.pdb'\n",
    "                local_file = f'Data/Chess/pdb_v1.2/{chess_dict[id]}.pdb'\n",
    "                if os.path.isfile(local_file):\n",
    "                    to_return.append(file)\n",
    "    if to_return:\n",
    "        return to_return\n",
    "    else:\n",
    "        print (\"NO AF2 Models found\")\n",
    "        return 0\n",
    "        \n",
    "print (get_af2s('CD44'))\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.3.pdb', 'C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.6.pdb', 'C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.alt117.pdb', 'C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.7.pdb', 'C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.alt116.pdb', 'C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.4.pdb', 'C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.5.pdb', 'C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.1.pdb', 'C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.alt100.pdb']\n"
     ]
    }
   ],
   "source": [
    "def get_all_af2s(gene):\n",
    "    to_return = []\n",
    "    name_key = {}\n",
    "    ensts = []\n",
    "    ref,nonref = ref_nonref(gene)\n",
    "    # Get ref[0]\n",
    "    ensts.append( name_enst [ref[0]].split('.')[0] )\n",
    "    #print (f\"ref is {ensts[0].split('.')[0]}\")\n",
    "    for nr in nonref:\n",
    "        if nr in name_enst:\n",
    "            ensts.append( name_enst[nr].split('.')[0] )\n",
    "            #print (f\"nr is {name_enst[nr].split('.')[0]}\") \n",
    "    for id in ensts:\n",
    "        if id in chess_dict:\n",
    "            file=f'{chess_pdb_dir}/{chess_dict[id]}.pdb'\n",
    "            local_file = f'Data/Chess/pdb_v1.2/{chess_dict[id]}.pdb'\n",
    "            if os.path.isfile(local_file):\n",
    "                to_return.append(file)\n",
    "    if to_return:\n",
    "        return to_return\n",
    "    else:\n",
    "        print (\"NO AF2 Models found\")\n",
    "        return 0\n",
    "        \n",
    "print (get_all_af2s('CD44'))\n",
    "    "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## ChimeraX stuff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "os.getcwd()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The longest reference isoform is 2i83_A\n",
      "ChimeraX script written. Use open \"C:/Users/daroc/Documents/Work/Structures/Chimerax/CD44.cxc\" \n",
      "close session\n",
      "cd C:/Users/daroc/Documents/Work/Structures/Chimerax\n",
      "set bgcolor white\n",
      "ui mousemode right pivot\n",
      "open 2i83\n",
      " hide #1 cartoons\n",
      " hide #1 atoms\n",
      " show #1/A cartoons\n",
      " color #1/A rgb(35,45,75)\n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.3.pdb\"\n",
      " hide #2 cartoons\n",
      " hide #2 atoms\n",
      " show #2 cartoons\n",
      " mm #2 to #1/A\n",
      " color #2 rgb(229,114,0)\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.6.pdb\"\n",
      " hide #3 cartoons\n",
      " hide #3 atoms\n",
      " show #3 cartoons\n",
      " mm #3 to #1/A\n",
      " color #3 dark green\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.alt117.pdb\"\n",
      " hide #4 cartoons\n",
      " hide #4 atoms\n",
      " show #4 cartoons\n",
      " mm #4 to #1/A\n",
      " color #4 yellow\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.7.pdb\"\n",
      " hide #5 cartoons\n",
      " hide #5 atoms\n",
      " show #5 cartoons\n",
      " mm #5 to #1/A\n",
      " color #5 indigo\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.alt116.pdb\"\n",
      " hide #6 cartoons\n",
      " hide #6 atoms\n",
      " show #6 cartoons\n",
      " mm #6 to #1/A\n",
      " color #6 maroon\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.4.pdb\"\n",
      " hide #7 cartoons\n",
      " hide #7 atoms\n",
      " show #7 cartoons\n",
      " mm #7 to #1/A\n",
      " color #7 dark turquoise\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.5.pdb\"\n",
      " hide #8 cartoons\n",
      " hide #8 atoms\n",
      " show #8 cartoons\n",
      " mm #8 to #1/A\n",
      " color #8 saddle brown\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.1.pdb\"\n",
      " hide #9 cartoons\n",
      " hide #9 atoms\n",
      " show #9 cartoons\n",
      " mm #9 to #1/A\n",
      " color #9 dodger blue\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.alt100.pdb\"\n",
      " hide #10 cartoons\n",
      " hide #10 atoms\n",
      " show #10 cartoons\n",
      " mm #10 to #1/A\n",
      " color #10 deep pink\n",
      "        \n",
      "open \"c:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Seq_groups/CD44.aln\"\n",
      " view\n",
      " #Structres for CD44\n",
      "save \"C:/Users/daroc/Documents/Work/Structures/Chimerax/CD44.png\"  transparentBackground  true\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Relies on blast_df\n",
    "chimerax_dir = 'C:/Users/daroc/Documents/Work/Structures/Chimerax'\n",
    "posix_chimerax_dir = '/mnt/c/Users/daroc/Documents/Work/Structures/Chimerax'\n",
    "\n",
    "color_pairs = [('rgb(35,45,75)', 'medium blue') , ('rgb(229,114,0)', 'orange' ), ('dark green','lime green'), ('yellow','khaki'),\n",
    "               ('indigo','blue violet'), ('maroon', 'firebrick'), ('dark turquoise', 'cyan'), ('saddle brown','chocolate'),\n",
    "               ('dodger blue', 'sky blue'), ('deep pink', 'hot pink'), ('dim grey', 'grey'), ('olive','chartreus')              \n",
    "              ]\n",
    "color_pairs = color_pairs + color_pairs\n",
    "\n",
    "def split_chains(pdbs):\n",
    "    to_return = []\n",
    "    for pdb in pdbs: \n",
    "        #print (pdb)\n",
    "        p= re.split('_|,',pdb)\n",
    "        to_return.append((p[0],p[1]))\n",
    "    return ( to_return)\n",
    "def get_ref_pdb(gene):\n",
    "    \"\"\"Finds longest reference & returns a 1 ently list. The sole record is (pdb,chain)\"\"\"\n",
    "    ref_blast = blast_df.loc[ blast_df['qseqid'].isin(pdb_ref_list_by_gene[gene])]\n",
    "    longest_ref = ref_blast.loc[ref_blast['length'].idxmax()]['qseqid']\n",
    "    print (f'The longest reference isoform is {longest_ref}')\n",
    "    return split_chains([longest_ref])\n",
    "def get_iso_pdbs(gene):\n",
    "    \"\"\"Returns a dict {pdb:chain} for isos with distinct length\"\"\"\n",
    "    ref,nonref = ref_nonref(gene)\n",
    "    #df = blast_df.loc[ blast_df['qseqid'].isin(pdb_nonref_list_by_gene[gene])]\n",
    "    df = blast_df.loc[ blast_df['qseqid'].isin(nonref)]\n",
    "    df_lowest_index_by_length = df.groupby('length')['length'].idxmin()\n",
    "    #print (df_lowest_index_by_length)\n",
    "    result_df = df.loc[df_lowest_index_by_length]\n",
    "    isos =  split_chains(result_df['qseqid'].unique())\n",
    "    return isos\n",
    "def get_all_iso_pdbs(gene):\n",
    "    \"\"\"Returns a dict {pdb:chain} for isos with distinct length\"\"\"\n",
    "    ref,nonref = ref_nonref(gene)\n",
    "    df = blast_df.loc[ blast_df['qseqid'].isin(nonref)]\n",
    "    isos =  split_chains(df['qseqid'].unique())\n",
    "    return isos   \n",
    "#print (get_all_iso_pdbs('CCR2'))\n",
    "def get_af2s(gene):\n",
    "    to_return = []\n",
    "    ref,nonref = ref_nonref(gene)\n",
    "    #df = blast_df.loc[ blast_df['qseqid'].isin(pdb_nonref_list_by_gene[gene])]\n",
    "    df = blast_df.loc[ blast_df['qseqid'].isin(nonref)]\n",
    "    df2 = df.loc[df.groupby('qseqid')['bitscore'].idxmax()]\n",
    "    af2_ids = df2['sseqid'].map(gene_hash).unique()\n",
    "    if len(af2_ids) > 0:\n",
    "        for id in af2_ids:\n",
    "            if id in chess_dict:\n",
    "                file=f'{chess_pdb_dir}/{chess_dict[id]}.pdb'\n",
    "                local_file = f'Data/Chess/pdb_v1.2/{chess_dict[id]}.pdb'\n",
    "                if os.path.isfile(local_file):\n",
    "                    to_return.append(file)\n",
    "    if to_return:\n",
    "        return to_return\n",
    "    else:\n",
    "        print (\"NO AF2 Models found\")\n",
    "        return 0\n",
    "    \n",
    "def get_all_af2s(gene):\n",
    "    to_return = []\n",
    "    name_key = {}\n",
    "    ensts = []\n",
    "    ref,nonref = ref_nonref(gene)\n",
    "    # Get ref[0]\n",
    "    ensts.append( name_enst [ref[0]].split('.')[0] )\n",
    "    #print (f\"ref is {ensts[0].split('.')[0]}\")\n",
    "    for nr in nonref:\n",
    "        if nr in name_enst:\n",
    "            ensts.append( name_enst[nr].split('.')[0] )\n",
    "            #print (f\"nr is {name_enst[nr].split('.')[0]}\") \n",
    "    for id in ensts:\n",
    "        if id in chess_dict:\n",
    "            file=f'{chess_pdb_dir}/{chess_dict[id]}.pdb'\n",
    "            local_file = f'Data/Chess/pdb_v1.2/{chess_dict[id]}.pdb'\n",
    "            if os.path.isfile(local_file):\n",
    "                to_return.append(file)\n",
    "    if to_return:\n",
    "        return to_return\n",
    "    else:\n",
    "        print (\"NO AF2 Models found\")\n",
    "        return 0      \n",
    "    \n",
    "        \n",
    "def chimerax(gene):\n",
    "    # Reference isoform stuff\n",
    "    ref_pdb = get_ref_pdb(gene)\n",
    "\n",
    "    #print (ref_pdb, isos)\n",
    "    cx = f\"\"\"close session\n",
    "cd C:/Users/daroc/Documents/Work/Structures/Chimerax\n",
    "set bgcolor white\n",
    "ui mousemode right pivot\n",
    "\"\"\"\n",
    "    \n",
    "    cx += f\"\"\"open {ref_pdb[0][0]}\n",
    " hide #1 cartoons\n",
    " hide #1 atoms\n",
    " show #1/{ref_pdb[0][1]} cartoons\n",
    " color #1/{ref_pdb[0][1]} {color_pairs[0][0]}\n",
    "\"\"\"\n",
    "    # Iso forms\n",
    "    isos = get_all_iso_pdbs(gene)\n",
    "    count = 2\n",
    "    for iso in isos:\n",
    "        cx += f\"\"\"open {iso[0]}\n",
    " hide #{count} cartoons\n",
    " hide #{count} atoms\n",
    " show #{count}/{iso[1]} cartoons\n",
    " mm #{count}/{iso[1]} to #1/{ref_pdb[0][1]}\n",
    " color #{count}/{iso[1]} {color_pairs[count-1][0]}\n",
    "\"\"\"\n",
    "        count += 1\n",
    "\n",
    "\n",
    "    # AF2 stuff\n",
    "    af2s = get_all_af2s(gene)\n",
    "    if af2s:\n",
    "        for af2 in af2s:\n",
    "            cx += f\"\"\"\n",
    "open \"{af2}\"\n",
    " hide #{count} cartoons\n",
    " hide #{count} atoms\n",
    " show #{count} cartoons\n",
    " mm #{count} to #1/{ref_pdb[0][1]}\n",
    " color #{count} {color_pairs[count-1][0]}\n",
    "        \n",
    "\"\"\"\n",
    "            count += 1\n",
    "# END AF2 Stuff \n",
    "\n",
    "    cx += f\"\"\"open \"c:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/{data_dir}/{gene}.aln\"\\n \"\"\"\n",
    "    cx += f\"\"\"view\\n #Structres for {gene}\n",
    "save \"C:/Users/daroc/Documents/Work/Structures/Chimerax/{gene}.png\"  transparentBackground  true\n",
    "\"\"\"\n",
    "    if os.name == 'posix':\n",
    "        cxdir =posix_chimerax_dir\n",
    "    else:\n",
    "        cxdir = chimerax_dir\n",
    "    cxc_file = f'{cxdir}/{gene}.cxc'\n",
    "    with open (cxc_file, 'w') as out:\n",
    "        out.write(cx)\n",
    "    print (f\"\"\"ChimeraX script written. Use open \"{chimerax_dir}/{gene}.cxc\" \"\"\")    \n",
    "    return (cx)\n",
    "    \n",
    "    \n",
    "\n",
    "    \n",
    "cxc = chimerax('CD44')\n",
    "print (cxc)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CD44-206\n",
      "ENST is ENST00000415148\n",
      "Chess ref is CHS.8449.3\n",
      "ref_CD44-206\tCHS.8449.3\n",
      "alt_CD44-201\tCHS.8449.6\n",
      "alt_CD44-203\tCHS.8449.alt117\n",
      "alt_CD44-205\tCHS.8449.7\n",
      "alt_CD44-208\tCHS.8449.alt116\n",
      "alt_CD44-209\tCHS.8449.4\n",
      "alt_CD44-210\tCHS.8449.5\n",
      "alt_CD44-211\tCHS.8449.1\n",
      "alt_CD44-222\tCHS.8449.alt100\n"
     ]
    }
   ],
   "source": [
    "def chess_for_gene(gene, print_it = True):\n",
    "    to_return = {}\n",
    "    ref,nonref = ref_nonref(gene)\n",
    "    for name in ref:\n",
    "        print (name)\n",
    "        enst = name_enst[name].split('.')[0]\n",
    "        print (f'ENST is {enst}')\n",
    "        if enst in chess_dict:\n",
    "            chess = chess_dict[enst]\n",
    "            to_return[f'ref_{name}'] = chess\n",
    "            print (f'Chess ref is {chess}')\n",
    "    for name in nonref:\n",
    "        if name in name_enst:\n",
    "            enst = name_enst[name].split('.')[0]\n",
    "            if enst in chess_dict:\n",
    "                chess = chess_dict[enst]\n",
    "                to_return[f'alt_{name}'] =  chess\n",
    "                \n",
    "    if print_it:\n",
    "        for i,v in to_return.items():\n",
    "            print (f'{i}\\t{v}')\n",
    "    return to_return\n",
    "                      \n",
    "name_key = chess_for_gene('CD44')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ENST00000415148.6\n",
      "CHS.8449.3\n",
      "(['CD44-206'], ['CD44-201', 'CD44-202', 'CD44-203', 'CD44-204', 'CD44-205', 'CD44-207', 'CD44-208', 'CD44-209', 'CD44-210', 'CD44-211', 'CD44-212', 'CD44-213', 'CD44-214', 'CD44-215', 'CD44-216', 'CD44-217', 'CD44-218', 'CD44-219', 'CD44-220', 'CD44-221', 'CD44-222', 'CD44-223', 'CD44-224', 'CD44-225', 'CD44-226', 'CD44-227', 'CD44-228', 'CD44-229', 'CD44-230', 'CD44-231', 'CD44-232', 'CD44-233', 'CD44-234', 'CD44-235', 'CD44-236', 'CD44-237', 'CD44-238'])\n"
     ]
    }
   ],
   "source": [
    "print (name_enst['CD44-206'])\n",
    "print (chess_dict['ENST00000415148'])\n",
    "print (ref_nonref('CD44'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Multi-output cell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "{'CCDC92', 'PRDM16', 'ITGA1', 'MRAS', 'EHMT2', 'CENPW', 'NOB1', 'NT5C2', 'PARP12', 'ZNF664', 'SMG6', 'RP11-214K3.25', 'DHX58', 'RAB5C', 'SREBF1', 'OAZ3', 'WIPI1'}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print (chimerax(gene))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "open \"C:/Users/daroc/Documents/Work/Structures/Chimerax/CD44.cxc\" \n",
      "(['CD44-206'], ['CD44-201', 'CD44-202', 'CD44-203', 'CD44-204', 'CD44-205', 'CD44-207', 'CD44-208', 'CD44-209', 'CD44-210', 'CD44-211', 'CD44-212', 'CD44-213', 'CD44-214', 'CD44-215', 'CD44-216', 'CD44-217', 'CD44-218', 'CD44-219', 'CD44-220', 'CD44-221', 'CD44-222', 'CD44-223', 'CD44-224', 'CD44-225', 'CD44-226', 'CD44-227', 'CD44-228', 'CD44-229', 'CD44-230', 'CD44-231', 'CD44-232', 'CD44-233', 'CD44-234', 'CD44-235', 'CD44-236', 'CD44-237', 'CD44-238'])\n",
      "Matchces for gene\n",
      "         qseqid qlen qstart qend    sseqid slen sstart send    evalue bitscore  \\\n",
      "351     1poz_A  159    115  155  CD44-219  243      2   42  7.56e-23     92.0   \n",
      "4552    2i83_A  160    116  156  CD44-219  243      2   42  6.66e-23     92.0   \n",
      "256   4pz3_A,B  153    110  153  CD44-231  268      1   44  2.94e-25     98.6   \n",
      "257   4pz4_A,B  154    110  154  CD44-231  268      1   45  8.37e-26      100   \n",
      "\n",
      "     length nident gaps gapopen mismatch   pident  gene  \n",
      "351      41     41    0       0        0  100.000  CD44  \n",
      "4552     41     41    0       0        0  100.000  CD44  \n",
      "256      44     44    0       0        0  100.000  CD44  \n",
      "257      45     45    0       0        0  100.000  CD44  \n",
      "\n",
      "\n",
      " >2i83_A\n",
      "MAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDV\n",
      ">1poz_A\n",
      "AQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDV\n",
      ">4pz3_A,B\n",
      "AMAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYP\n",
      ">4pz4_A,B\n",
      "AMAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPS\n",
      ">REF_CD44-206\n",
      "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATSTSSNTISAGWEPNEENEDERDRHLSFSGSGIDDDEDFISSTISTTPRAFDHTKQNQDWTQWNPSHSNPEVLLQTTTRMTDVDRNGTTAYEGNWNPEAHPPLIHHEHHEEEETPHSTSTIQATPSSTTEETATQKEQWFGNRWHEGYRQTPKEDSHSTTGTAAASAHTSHPMQGRTTPSPEDSSWTDFFNPISHPMGRGHQAGRRMDMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRNDVTGGRRDPNHSEGSTTLLEGYTSHYPHTKESRTFIPVTSAKTGSFGVTAVTVGDSNSNVNRSLSGDQDTFHPSGGSHTTHGSESDGHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAVNSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADETRNLQNVDMKIGV\n",
      ">ALT_CD44-219\n",
      "XDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATTLMSTSATATETATKRQETWDWFSWLFLPSESKNHLHTTTQMAGTSSNTISAGWEPNEENEDERDRHLSFSGSGIDDDEDFISSTNMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRND\n",
      ">ALT_CD44-231\n",
      "EDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSSGSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATIQATPSSTTEETATQKEQWFGNRWHEGYRQTPKEDSHSTTGTAAASAHTSHPMQGRTTPSPEDSSWTDFFNPISHPMGRGHQAGRRMDMDSSHSITLQPTANPNTGLVEDLDRTGPLSMTTQQSNSQSFSTSHEGLEEDKDHPTTSTLTSSNRNDVTGGRRDPNHSEGSTTL\n",
      "\n",
      "CLUSTAL O(1.2.4) multiple sequence alignment\n",
      "\n",
      "\n",
      "1poz_A                          -------------------AQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTL\n",
      "4pz3_A,B                        -----------------AMAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTL\n",
      "4pz4_A,B                        -----------------AMAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTL\n",
      "2i83_A                          ------------------MAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTL\n",
      "CD44-211|ENST00000442151.6      XDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTL\n",
      "CD44-214|ENST00000525211.6      MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTL\n",
      "CD44-205|ENST00000352818.8      MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTL\n",
      "                                                   *****************************************\n",
      "\n",
      "1poz_A                          PTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFN\n",
      "4pz3_A,B                        PTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFN\n",
      "4pz4_A,B                        PTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFN\n",
      "2i83_A                          PTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFN\n",
      "CD44-211|ENST00000442151.6      PTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFN\n",
      "CD44-214|ENST00000525211.6      PTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFN\n",
      "CD44-205|ENST00000352818.8      PTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFN\n",
      "                                ************************************************************\n",
      "\n",
      "1poz_A                          ASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDV--\n",
      "4pz3_A,B                        ASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYP----------\n",
      "4pz4_A,B                        ASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPS---------\n",
      "2i83_A                          ASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDV--\n",
      "CD44-211|ENST00000442151.6      ASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSS\n",
      "CD44-214|ENST00000525211.6      ASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSS\n",
      "CD44-205|ENST00000352818.8      ASAPPEEDCTSVTDLPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDVSS\n",
      "                                **************************************************          \n",
      "\n",
      "1poz_A                          ------------------------------------------------------------\n",
      "4pz3_A,B                        ------------------------------------------------------------\n",
      "4pz4_A,B                        ------------------------------------------------------------\n",
      "2i83_A                          ------------------------------------------------------------\n",
      "CD44-211|ENST00000442151.6      GSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATRDQD-TFHPSGGSHTTHG\n",
      "CD44-214|ENST00000525211.6      GSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATTASAHTSHPMQGRTTPSP\n",
      "CD44-205|ENST00000352818.8      GSSSERSSTSGGYIFYTFSTVHPIPDEDSPWITDSTDRIPATR-----------------\n",
      "                                                                                            \n",
      "\n",
      "1poz_A                          ------------------------------------------------------------\n",
      "4pz3_A,B                        ------------------------------------------------------------\n",
      "4pz4_A,B                        ------------------------------------------------------------\n",
      "2i83_A                          ------------------------------------------------------------\n",
      "CD44-211|ENST00000442151.6      SESD----------GHSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAV\n",
      "CD44-214|ENST00000525211.6      EDSSWTDFFNPISHPMGRGHQAGRRMDMDS--------SHSITLQ---------------\n",
      "CD44-205|ENST00000352818.8      ---------------HSHGSQEGGANTTSGPIRTPQIPEWLIILASLLALALILAVCIAV\n",
      "                                                                                            \n",
      "\n",
      "1poz_A                          ------------------------------------------------------------\n",
      "4pz3_A,B                        ------------------------------------------------------------\n",
      "4pz4_A,B                        ------------------------------------------------------------\n",
      "2i83_A                          ------------------------------------------------------------\n",
      "CD44-211|ENST00000442151.6      NSRRS-------------------------------------------------------\n",
      "CD44-214|ENST00000525211.6      ------------------------------------------------------------\n",
      "CD44-205|ENST00000352818.8      NSRRRCGQKKKLVINSGNGAVEDRKPSGLNGEASKSQEMVHLVNKESSETPDQFMTADET\n",
      "                                                                                            \n",
      "\n",
      "1poz_A                          ------------\n",
      "4pz3_A,B                        ------------\n",
      "4pz4_A,B                        ------------\n",
      "2i83_A                          ------------\n",
      "CD44-211|ENST00000442151.6      ------------\n",
      "CD44-214|ENST00000525211.6      ------------\n",
      "CD44-205|ENST00000352818.8      RNLQNVDMKIGV\n",
      "                                            \n",
      "\n",
      "The longest reference isoform is 2i83_A\n",
      "ChimeraX script written. Use open \"C:/Users/daroc/Documents/Work/Structures/Chimerax/CD44.cxc\" \n",
      "close session\n",
      "cd C:/Users/daroc/Documents/Work/Structures/Chimerax\n",
      "set bgcolor white\n",
      "ui mousemode right pivot\n",
      "open 2i83\n",
      " hide #1 cartoons\n",
      " hide #1 atoms\n",
      " show #1/A cartoons\n",
      " color #1/A rgb(35,45,75)\n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.3.pdb\"\n",
      " hide #2 cartoons\n",
      " hide #2 atoms\n",
      " show #2 cartoons\n",
      " mm #2 to #1/A\n",
      " color #2 rgb(229,114,0)\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.6.pdb\"\n",
      " hide #3 cartoons\n",
      " hide #3 atoms\n",
      " show #3 cartoons\n",
      " mm #3 to #1/A\n",
      " color #3 dark green\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.alt117.pdb\"\n",
      " hide #4 cartoons\n",
      " hide #4 atoms\n",
      " show #4 cartoons\n",
      " mm #4 to #1/A\n",
      " color #4 yellow\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.7.pdb\"\n",
      " hide #5 cartoons\n",
      " hide #5 atoms\n",
      " show #5 cartoons\n",
      " mm #5 to #1/A\n",
      " color #5 indigo\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.alt116.pdb\"\n",
      " hide #6 cartoons\n",
      " hide #6 atoms\n",
      " show #6 cartoons\n",
      " mm #6 to #1/A\n",
      " color #6 maroon\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.4.pdb\"\n",
      " hide #7 cartoons\n",
      " hide #7 atoms\n",
      " show #7 cartoons\n",
      " mm #7 to #1/A\n",
      " color #7 dark turquoise\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.5.pdb\"\n",
      " hide #8 cartoons\n",
      " hide #8 atoms\n",
      " show #8 cartoons\n",
      " mm #8 to #1/A\n",
      " color #8 saddle brown\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.1.pdb\"\n",
      " hide #9 cartoons\n",
      " hide #9 atoms\n",
      " show #9 cartoons\n",
      " mm #9 to #1/A\n",
      " color #9 dodger blue\n",
      "        \n",
      "\n",
      "open \"C:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Chess/pdb_v1.2/CHS.8449.alt100.pdb\"\n",
      " hide #10 cartoons\n",
      " hide #10 atoms\n",
      " show #10 cartoons\n",
      " mm #10 to #1/A\n",
      " color #10 deep pink\n",
      "        \n",
      "open \"c:/Users/daroc/OneDrive - University of Virginia/Sheynkman/Python/Pdb-isoform-analysis/Data/Seq_groups/CD44.aln\"\n",
      " view\n",
      " #Structres for CD44\n",
      "save \"C:/Users/daroc/Documents/Work/Structures/Chimerax/CD44.png\"  transparentBackground  true\n",
      "\n"
     ]
    }
   ],
   "source": [
    "gene = 'CD44'\n",
    "\n",
    "print (f\"\"\"open \"C:/Users/daroc/Documents/Work/Structures/Chimerax/{gene}.cxc\" \"\"\")\n",
    "print (ref_nonref(gene))\n",
    "\n",
    "print (\"Matchces for gene\\n\", matches_for_gene(gene) )\n",
    "print (\"\\n\\n\",pdbs_with_appris(gene))\n",
    "one_msa(gene)\n",
    "\n",
    "print (chimerax(gene))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "gene = 'CASP1'\n",
    "\n",
    "print (f\"\"\"open \"C:/Users/daroc/Documents/Work/Structures/Chimerax/{gene}.cxc\" \"\"\")\n",
    "print (ref_nonref(gene))\n",
    "\n",
    "print (\"Matchces for gene\\n\", matches_for_gene(gene) )\n",
    "print (\"\\n\\n\",pdbs_with_appris(gene))\n",
    "one_msa(gene)\n",
    "\n",
    "print (chimerax(gene))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "gene = 'CASP1'\n",
    "\n",
    "print (f\"\"\"open \"C:/Users/daroc/Documents/Work/Structures/Chimerax/{gene}.cxc\" \"\"\")\n",
    "print (ref_nonref(gene))\n",
    "\n",
    "print (\"Matchces for gene\\n\", matches_for_gene(gene) )\n",
    "print (\"\\n\\n\",pdbs_with_appris(gene))\n",
    "one_msa(gene)\n",
    "\n",
    "print (chimerax(gene))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print (matches_for_gene(gene, blast_df) )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Group by genes\n",
    "## Note IGHG1 is IGG heavy chain\n",
    "npp_g2=non_appris_pdbs.groupby('gene', as_index = False) ['qseqid'].nunique()\n",
    "npp_g2 = npp_g2.rename(columns={'qseqid':'count'}).sort_values(by=['count'], ascending =False)\n",
    "npp_g2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "npp_g=non_appris_pdbs.groupby('gene', as_index = False) ['sseqid'].nunique()\n",
    "npp_g = npp_g.rename(columns={'sseqid':'count'}).sort_values(by=['count'], ascending =False)\n",
    "npp_g"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Export cell output to a file \n",
    "\n",
    "Cell 1  \n",
    "<code>\n",
    "    %%capture cap --no-stderr\n",
    "    print(q)\n",
    "</code>\n",
    "\n",
    "Cell 2  \n",
    "<code>\n",
    "with open('output.txt', 'w') as f:    \n",
    "    f.write(cap.stdout)\n",
    "    </code>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Function to reduce the data to top matches of each PDB\n",
    "Function is called top_five, the the second option is the numner of hits to include"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def top_five(df, max=5 ):\n",
    "    keep= []\n",
    "    last = \"\"\n",
    "    for i,row in df.iterrows():\n",
    "        if row['qseqid'] != last:\n",
    "            count=1\n",
    "            last = row['qseqid']\n",
    "            keep.append(True)\n",
    "        else:\n",
    "            count += 1\n",
    "            if count<=max:\n",
    "                keep.append(True)\n",
    "            else:\n",
    "                keep.append(False)\n",
    "    return (df.loc[keep])\n",
    "#top_five_df = top_five(copy_df)\n",
    "#top_five_df.to_excel('top5_pdb_vs_gencode.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def top_five_bitscore(df, max=5 ):\n",
    "    keep= []\n",
    "    last = \"\"\n",
    "    for i,row in df.iterrows():\n",
    "        if row['qseqid'] != last:\n",
    "            count=1\n",
    "            last = row['qseqid']\n",
    "            bitscore_threshold  = row['bitscore'] * 0.95\n",
    "            keep.append(True)\n",
    "        else:\n",
    "            count += 1\n",
    "            if count<=max and row['bitscore'] > bitscore_threshold:\n",
    "                keep.append(True)\n",
    "            else:\n",
    "                keep.append(False)\n",
    "    return (df.loc[keep])\n",
    "#bitscore_df = top_five_bitscore(blast_df)\n",
    "#bitscore_df\n",
    "#top_five_df.to_excel('top5_pdb_vs_gencode.xlsx')\n",
    "\n",
    "## This will find all isoforms that \n",
    "def top_five_bitscore_exact(df, max=5 ):\n",
    "    keep= []\n",
    "    last = \"\"\n",
    "    for i,row in df.iterrows():\n",
    "        if row['qseqid'] != last:\n",
    "            count=1\n",
    "            last = row['qseqid']\n",
    "            bitscore_threshold  = row['bitscore'] \n",
    "            keep.append(True)\n",
    "        else:\n",
    "            count += 1\n",
    "            if row['bitscore'] == bitscore_threshold and count<=max:\n",
    "                keep.append(True)\n",
    "            else:\n",
    "                keep.append(False)\n",
    "    return (df.loc[keep])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "top_100_matched = top_five_bitscore_exact(blast_df, 100)\n",
    "top_100_matched"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "top_100_list = []\n",
    "for i,row in top_100_matched.iterrows():\n",
    "    top_100_list.append(row.tolist())\n",
    "print (top_100_list[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print (top_100_list[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "top_100_matched.to_csv('Data/top_100_matched.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb_to_gencode[0]\n",
    "#pdb_grouped_by_qseqid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb_to_gencode = []\n",
    "with open('Data/blast_full_PDB_vs_gencode.tsv', 'r') as pdb_file:\n",
    "    pdb_reader = csv.reader(pdb_file, delimiter='\\t')\n",
    "    next(pdb_reader, None)\n",
    "    for row in pdb_reader:\n",
    "        row[5] = row[5].split('|')[0]\n",
    "        pdb_to_gencode.append(row)\n",
    "    print (len (pdb_to_gencode))\n",
    "print (pdb_to_gencode[0:2])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "one_msa('CCR2')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "show_msa(to_inspect, fresh =0, last='EPHA7')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "show_msa(['HARS1'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "functional=pd.read_csv('Data/APPRIS_FunctionalTableLong.tsv',sep ='\\t')\n",
    "functional_genes = functional['HGNC'].tolist()\n",
    "functional_genes\n",
    "show_msa(functional_genes,fresh=0, last='ITGA7')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "functional=pd.read_csv('Data/Tandem_exon_derived_substitution_HES_APPRIS_functional.tsv',sep ='\\t')\n",
    "functional_genes = functional['HGNC'].tolist()\n",
    "functional_genes\n",
    "show_msa(functional_genes,fresh=1)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Below here extra   \n",
    "mirage, exonerate\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "blast_df.groupby(['qseqid'])['sseqid'].aggregate(lambda x: list(x)).reset_index()\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Identify genes with more than one isoform. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "genes_dict={}\n",
    "def multiple_isos(df):\n",
    "    genes=defaultdict(set)\n",
    "    # Build a dictionary where the values are a set of isoforms for each gene\n",
    "    for id in df['sseqid']:\n",
    "        try:\n",
    "            id = id.split('|')[0]\n",
    "            parts = id.split('-')\n",
    "            gene='-'.join(parts[0:-1])\n",
    "            iso=parts[-1]\n",
    "            #print (id, gene, iso)\n",
    "            genes[gene].add(iso)\n",
    "        except:\n",
    "            pass\n",
    "    # Create a list (check) of genes that have more than 1 isoform represented.\n",
    "    check = []\n",
    "    for g,g_set in genes.items():\n",
    "        if len(g_set) > 1:\n",
    "            check.append(g)\n",
    "            genes_dict[g]=g_set\n",
    "    print (f'check is {len(check)} long')\n",
    "\n",
    "    # Create list of df indicies of all genes that have more than one df \n",
    "    found=[]\n",
    "    for i,row in df.iterrows():\n",
    "        #print (row['sseqid'].split('-')[0])\n",
    "        try:\n",
    "            if row['sseqid'].split('-')[0] in check:\n",
    "                found.append(i)\n",
    "        except:\n",
    "            pass\n",
    "    #print (f'found is {found}')\n",
    "    found_df = df.loc[found]\n",
    "    found_df.sort_values(by=['sseqid'], inplace=True)\n",
    "    return found_df\n",
    "\n",
    "found_df = multiple_isos(top_100_matched)\n",
    "found_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Find genes that have a structures that match ref and non-ref isoforms \n",
    "Note: genes_dict will only contain genes that match more than one isoform."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "to_inspect=[]\n",
    "#for k in list(genes_dict.keys())[0:10]:\n",
    "for k in genes_dict:\n",
    "    try:\n",
    "        r,nr=ref_nonref(k)\n",
    "        r_iso = r.split('-')[1]\n",
    "        if r_iso in genes_dict[k]:\n",
    "            to_inspect.append(k)\n",
    "    except Exception as e:\n",
    "        pass\n",
    "\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "columns =  ['qseqid','qlen', 'qstart', 'qend', 'sseqid', 'slen', 'sstart', 'send', 'evalue', 'bitscore', 'length', 'nident', 'gaps','gapopen', 'mismatch', 'pident']\n",
    "filtered = pd.read_csv('Data/filtered_pdb_gencode_mapping.tsv', sep='\\t', index_col= False, header = None, names = columns)\n",
    "filtered"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Write out "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Write out the filtered mapping to a TSV file\n",
    "with open('Data/filtered_pdb_gencode_mapping.tsv', 'w') as output_file:\n",
    "    output_writer = csv.writer(output_file, delimiter='\\t')\n",
    "    for row in filtered_pdb_to_gencode:\n",
    "        output_writer.writerow(row)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "gene_dict= defaultdict(set)\n",
    "def seq_loop(df, dir ='Data/Seq_groups/' ):\n",
    "    gene_list = []\n",
    "    for id in df['sseqid']:\n",
    "        try:\n",
    "            id = id.split('|')[0]\n",
    "            parts = id.split('-')\n",
    "            gene='-'.join(parts[0:-1])\n",
    "            if gene not in gene_list:\n",
    "                gene_list.append(gene)\n",
    "                gene_dict[gene].add(id)\n",
    "                file = f'Data/Seq_groups/{gene}.fa'\n",
    "                if os.path.isfile(file):\n",
    "                    continue\n",
    "                s = get_gene_seqs(gene)\n",
    "                with open (f'{dir}/{gene}.fa', 'w') as out:\n",
    "                    out.write(s)\n",
    "        except:\n",
    "            pass\n",
    "    return (gene_list)\n",
    "gene_list=seq_loop(found_df, dir)\n",
    "#filtered_genes= pd.DataFrame(done)  \n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from tqdm.notebook import trange, tqdm\n",
    "keep = []\n",
    "last = \"\"\n",
    "for i, row in tqdm(blast_df.iterrows()):\n",
    "    if row['qseqid'] != last:\n",
    "        keep.append(True)\n",
    "        last = row['qseqid']\n",
    "    else:\n",
    "        keep.append(False)\n",
    "one_each = blast_df.loc[ keep]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def range_mm \n"
   ]
  }
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