Search_ncbi_and_clear_data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Carregar pacotes necessários\n",
    "from Bio import SeqIO   # Importar a função SeqIO do pacote Bio\n",
    "from Bio import AlignIO   # Importar a função AlignIO do pacote Bio\n",
    "from Bio import Entrez    # Importar a função Entrez do pacote Bio\n",
    "from collections import defaultdict   # Importar a função defaultdict do pacote collections\n",
    "import subprocess  # Importar a função subprocess\n",
    "import re   # Importar a função re\n",
    "import os    # Importar a função os\n",
    "\n",
    "# Configurar o e-mail para acessar o NCBI\n",
    "Entrez.email = \"nathanpaivab@gmail.com\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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      "Salvo: EU017577_EU018044_sequences/EU017900.1_Ischnocnema_aff._ramagii_ACC_JMB2007a_cytb.fasta\n",
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      "Salvo: EU017577_EU018044_sequences/EU017903.1_Ischnocnema_aff._ramagii_ACC_JMB2007a_cytb.fasta\n",
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      "Salvo: EU017577_EU018044_sequences/EU017913.1_Ischnocnema_aff._ramagii_ACC_JMB2007a_cytb.fasta\n",
      "Salvo: EU017577_EU018044_sequences/EU017914.1_Ischnocnema_aff._ramagii_ACC_JMB2007a_cytb.fasta\n",
      "Salvo: EU017577_EU018044_sequences/EU017915.1_Ischnocnema_aff._ramagii_ACC_JMB2007a_ND2.fasta\n",
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      "Salvo: EU017577_EU018044_sequences/EU018044.1_Ischnocnema_aff._ramagii_ACC_JMB2007c_ND2.fasta\n"
     ]
    }
   ],
   "source": [
    "\n",
    "\n",
    "def search_genes_ncbi_range(start_id, end_id):\n",
    "    \"\"\"\n",
    "    Pesquisa genes no NCBI a partir de um intervalo de códigos de identificação de genes.\n",
    "\n",
    "    Parameters:\n",
    "    start_id (str): Código de identificação do gene inicial no NCBI.\n",
    "    end_id (str): Código de identificação do gene final no NCBI.\n",
    "\n",
    "    Returns:\n",
    "    list: Lista de SeqRecord contendo as sequências dos genes.\n",
    "    \"\"\"\n",
    "    # Extrair prefixo e números dos IDs\n",
    "    prefix = re.match(r\"([A-Za-z]+)\", start_id).group(1)\n",
    "    start_num = int(re.match(r\"[A-Za-z]+(\\d+)\", start_id).group(1))\n",
    "    end_num = int(re.match(r\"[A-Za-z]+(\\d+)\", end_id).group(1))\n",
    "\n",
    "    gene_ids = [f\"{prefix}{i:06d}\" for i in range(start_num, end_num + 1)]\n",
    "\n",
    "    gene_records = []\n",
    "    for gene_id in gene_ids:\n",
    "        handle = Entrez.efetch(db=\"nucleotide\", id=gene_id, rettype=\"gb\", retmode=\"text\")\n",
    "        record = SeqIO.read(handle, \"genbank\")\n",
    "        handle.close()\n",
    "        gene_records.append(record)\n",
    "    return gene_records\n",
    "\n",
    "\n",
    "# Exemplo de uso\n",
    "start_id = \"EU017577\"\n",
    "end_id = \"EU018044\"\n",
    "\n",
    "\n",
    "gene_records = search_genes_ncbi_range(start_id, end_id)\n",
    "\n",
    "# Criar pasta para armazenar as sequências\n",
    "output_dir = f\"{start_id}_{end_id}_sequences\"\n",
    "os.makedirs(output_dir, exist_ok=True)\n",
    "\n",
    "for record in gene_records:\n",
    "    # Extrair o nome da espécie e do gene do GenBank\n",
    "    species_name = record.annotations.get(\"organism\", \"Unknown_species\").replace(\" \", \"_\")\n",
    "    gene_name = \"Unknown_gene\"\n",
    "    for feature in record.features:\n",
    "        if feature.type == \"CDS\" and \"gene\" in feature.qualifiers:\n",
    "            gene_name = feature.qualifiers[\"gene\"][0]\n",
    "            break\n",
    "\n",
    "    # Salvar cada sequência em um arquivo separado com o formato especificado\n",
    "    output_path = os.path.join(output_dir, f\"{record.id}_{species_name}_{gene_name}.fasta\")\n",
    "    SeqIO.write(record, output_path, \"fasta\")\n",
    "    print(f\"Salvo: {output_path}\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Salvo: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_concatenated.fasta\n",
      "Salvo: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_concatenated.fasta\n"
     ]
    }
   ],
   "source": [
    "#concatenar sequências de genes\n",
    "\n",
    "# Diretório onde as sequências estão armazenadas\n",
    "input_dir = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences\"\n",
    "\n",
    "# Dicionário para armazenar sequências por gene\n",
    "gene_sequences = defaultdict(list)\n",
    "\n",
    "# Iterar sobre os arquivos no diretório\n",
    "for filename in os.listdir(input_dir):\n",
    "    if filename.endswith(\".fasta\"):\n",
    "        filepath = os.path.join(input_dir, filename)\n",
    "        record = SeqIO.read(filepath, \"fasta\")\n",
    "        gene_name = filename.split('_')[-1].replace(\".fasta\", \"\")\n",
    "        gene_sequences[gene_name].append(record)\n",
    "\n",
    "# Concatenar sequências de cada gene em um único arquivo\n",
    "for gene_name, records in gene_sequences.items():\n",
    "    output_path = os.path.join(input_dir, f\"{gene_name}_concatenated.fasta\")\n",
    "    SeqIO.write(records, output_path, \"fasta\")\n",
    "    print(f\"Salvo: {output_path}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Salvo: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_concatenated.fasta\n"
     ]
    }
   ],
   "source": [
    "#concatenar sequências de genes\n",
    "\n",
    "# Diretório onde as sequências estão armazenadas\n",
    "input_dir = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences\"\n",
    "\n",
    "# Dicionário para armazenar sequências por gene\n",
    "gene_sequences = defaultdict(list)\n",
    "\n",
    "# Iterar sobre os arquivos no diretório\n",
    "for filename in os.listdir(input_dir):\n",
    "    if filename.endswith(\".fasta\"):\n",
    "        filepath = os.path.join(input_dir, filename)\n",
    "        record = SeqIO.read(filepath, \"fasta\")\n",
    "        gene_name = filename.split('_')[-1].replace(\".fasta\", \"\")\n",
    "        gene_sequences[gene_name].append(record)\n",
    "\n",
    "# Concatenar sequências de cada gene em um único arquivo\n",
    "for gene_name, records in gene_sequences.items():\n",
    "    output_path = os.path.join(input_dir, f\"{gene_name}_concatenated.fasta\")\n",
    "    SeqIO.write(records, output_path, \"fasta\")\n",
    "    print(f\"Salvo: {output_path}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "ruby"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sequências filtradas salvas em: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei.fasta\n"
     ]
    }
   ],
   "source": [
    "#filtrar sequências de NAD2 apenas de Proceratophrys boiei\n",
    "\n",
    "\n",
    "# Caminho do arquivo concatenado\n",
    "input_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_concatenated.fasta\"\n",
    "output_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei.fasta\"\n",
    "\n",
    "# Ler as sequências do arquivo concatenado\n",
    "records = list(SeqIO.parse(input_file, \"fasta\"))\n",
    "\n",
    "# Filtrar sequências que pertencem à espécie Proceratophrys boiei\n",
    "filtered_sequences = [record for record in records if \"Proceratophrys boiei\" in record.description]\n",
    "\n",
    "# Salvar as sequências filtradas em um novo arquivo\n",
    "SeqIO.write(filtered_sequences, output_file, \"fasta\")\n",
    "\n",
    "print(f\"Sequências filtradas salvas em: {output_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "ruby"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sequências filtradas salvas em: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei.fasta\n"
     ]
    }
   ],
   "source": [
    "#filtrar sequências de cytb apenas de Proceratophrys boiei\n",
    "\n",
    "# Caminho do arquivo concatenado\n",
    "input_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_concatenated.fasta\"\n",
    "output_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei.fasta\"\n",
    "\n",
    "# Ler as sequências do arquivo concatenado\n",
    "records = list(SeqIO.parse(input_file, \"fasta\"))\n",
    "\n",
    "# Filtrar sequências que pertencem à espécie Proceratophrys boiei\n",
    "filtered_sequences = [record for record in records if \"Proceratophrys boiei\" in record.description]\n",
    "\n",
    "# Salvar as sequências filtradas em um novo arquivo\n",
    "SeqIO.write(filtered_sequences, output_file, \"fasta\")\n",
    "\n",
    "print(f\"Sequências filtradas salvas em: {output_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "ruby"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sequências filtradas salvas em: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei.fasta\n"
     ]
    }
   ],
   "source": [
    "#filtrar sequências de c-myc apenas de Proceratophrys boiei\n",
    "\n",
    "# Caminho do arquivo concatenado\n",
    "input_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_concatenated.fasta\"\n",
    "output_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei.fasta\"\n",
    "\n",
    "# Ler as sequências do arquivo concatenado\n",
    "records = list(SeqIO.parse(input_file, \"fasta\"))\n",
    "\n",
    "# Filtrar sequências que pertencem à espécie Proceratophrys boiei\n",
    "filtered_sequences = [record for record in records if \"Proceratophrys boiei\" in record.description]\n",
    "\n",
    "# Salvar as sequências filtradas em um novo arquivo\n",
    "SeqIO.write(filtered_sequences, output_file, \"fasta\")\n",
    "\n",
    "print(f\"Sequências filtradas salvas em: {output_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "ruby"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sequências renomeadas salvas em: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_renamed.fasta\n"
     ]
    }
   ],
   "source": [
    "#renomear as sequências de ND2 de Proceratophrys boiei para que fique apenas o código e o quinto termo do cabeçalho\n",
    "\n",
    "\n",
    "# Caminho do arquivo de entrada e saída\n",
    "input_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei.fasta\"\n",
    "output_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_renamed.fasta\"\n",
    "\n",
    "# Ler as sequências do arquivo de entrada\n",
    "records = list(SeqIO.parse(input_file, \"fasta\"))\n",
    "\n",
    "# Renomear os cabeçalhos das sequências\n",
    "for record in records:\n",
    "    description_parts = record.description.split()\n",
    "    sequence_id = description_parts[0]\n",
    "    fifth_term = description_parts[4] if len(description_parts) > 4 else \"\"\n",
    "    new_description = f\"{sequence_id} {fifth_term}\"\n",
    "    record.description = new_description\n",
    "    record.id = sequence_id  # Manter apenas o ID da sequência\n",
    "\n",
    "# Salvar as sequências com os novos cabeçalhos\n",
    "SeqIO.write(records, output_file, \"fasta\")\n",
    "\n",
    "print(f\"Sequências renomeadas salvas em: {output_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "ruby"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sequências renomeadas salvas em: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_renamed.fasta\n"
     ]
    }
   ],
   "source": [
    "#renomear as sequências de cytb de Proceratophrys boiei para que fique apenas o código e o quinto termo do cabeçalho\n",
    "\n",
    "# Caminho do arquivo de entrada e saída\n",
    "input_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei.fasta\"\n",
    "output_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_renamed.fasta\"\n",
    "\n",
    "# Ler as sequências do arquivo de entrada\n",
    "records = list(SeqIO.parse(input_file, \"fasta\"))\n",
    "\n",
    "# Renomear os cabeçalhos das sequências\n",
    "for record in records:\n",
    "    description_parts = record.description.split()\n",
    "    sequence_id = description_parts[0]\n",
    "    fifth_term = description_parts[4] if len(description_parts) > 4 else \"\"\n",
    "    new_description = f\"{sequence_id} {fifth_term}\"\n",
    "    record.description = new_description\n",
    "    record.id = sequence_id  # Manter apenas o ID da sequência\n",
    "\n",
    "# Salvar as sequências com os novos cabeçalhos\n",
    "SeqIO.write(records, output_file, \"fasta\")\n",
    "\n",
    "print(f\"Sequências renomeadas salvas em: {output_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "ruby"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sequências renomeadas salvas em: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_renamed.fasta\n"
     ]
    }
   ],
   "source": [
    "#renomear as sequências de ND2 de Proceratophrys boiei para que fique apenas o código e o quinto termo do cabeçalho\n",
    "\n",
    "# Caminho do arquivo de entrada e saída\n",
    "input_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei.fasta\"\n",
    "output_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_renamed.fasta\"\n",
    "\n",
    "# Ler as sequências do arquivo de entrada\n",
    "records = list(SeqIO.parse(input_file, \"fasta\"))\n",
    "\n",
    "# Renomear os cabeçalhos das sequências\n",
    "for record in records:\n",
    "    description_parts = record.description.split()\n",
    "    sequence_id = description_parts[0]\n",
    "    fifth_term = description_parts[4] if len(description_parts) > 4 else \"\"\n",
    "    new_description = f\"{sequence_id} {fifth_term}\"\n",
    "    record.description = new_description\n",
    "    record.id = sequence_id  # Manter apenas o ID da sequência\n",
    "\n",
    "# Salvar as sequências com os novos cabeçalhos\n",
    "SeqIO.write(records, output_file, \"fasta\")\n",
    "\n",
    "print(f\"Sequências renomeadas salvas em: {output_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "ruby"
    }
   },
   "outputs": [],
   "source": [
    "#caso queira as sequências de Proceratophrys boiei apenas com o número do voucher "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sequências renomeadas salvas em: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_renamed_second_term.fasta\n"
     ]
    }
   ],
   "source": [
    "#caso queira as sequências de Proceratophrys boiei apenas com o número do voucher \n",
    "# Caminho do arquivo de entrada e saída\n",
    "input_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_renamed.fasta\"\n",
    "output_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_renamed_second_term.fasta\"\n",
    "\n",
    "# Ler as sequências do arquivo de entrada\n",
    "records = list(SeqIO.parse(input_file, \"fasta\"))\n",
    "\n",
    "# Renomear os cabeçalhos das sequências\n",
    "for record in records:\n",
    "    description_parts = record.description.split()\n",
    "    second_term = description_parts[1] if len(description_parts) > 1 else \"\"\n",
    "    new_description = f\"{second_term}\"\n",
    "    record.description = new_description\n",
    "    record.id = second_term  # Manter apenas o segundo termo como ID da sequência\n",
    "\n",
    "# Salvar as sequências com os novos cabeçalhos\n",
    "SeqIO.write(records, output_file, \"fasta\")\n",
    "\n",
    "print(f\"Sequências renomeadas salvas em: {output_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sequências renomeadas salvas em: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_renamed_second_term.fasta\n"
     ]
    }
   ],
   "source": [
    "#caso queira as sequências de Proceratophrys boiei apenas com o número do voucher \n",
    "# Caminho do arquivo de entrada e saída\n",
    "input_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_renamed.fasta\"\n",
    "output_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_renamed_second_term.fasta\"\n",
    "\n",
    "# Ler as sequências do arquivo de entrada\n",
    "records = list(SeqIO.parse(input_file, \"fasta\"))\n",
    "\n",
    "# Renomear os cabeçalhos das sequências\n",
    "for record in records:\n",
    "    description_parts = record.description.split()\n",
    "    second_term = description_parts[1] if len(description_parts) > 1 else \"\"\n",
    "    new_description = f\"{second_term}\"\n",
    "    record.description = new_description\n",
    "    record.id = second_term  # Manter apenas o segundo termo como ID da sequência\n",
    "\n",
    "# Salvar as sequências com os novos cabeçalhos\n",
    "SeqIO.write(records, output_file, \"fasta\")\n",
    "\n",
    "print(f\"Sequências renomeadas salvas em: {output_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sequências renomeadas salvas em: /home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_renamed_second_term.fasta\n"
     ]
    }
   ],
   "source": [
    "#caso queira as sequências de Proceratophrys boiei apenas com o número do voucher \n",
    "# Caminho do arquivo de entrada e saída\n",
    "input_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_renamed.fasta\"\n",
    "output_file = \"/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_renamed_second_term.fasta\"\n",
    "\n",
    "# Ler as sequências do arquivo de entrada\n",
    "records = list(SeqIO.parse(input_file, \"fasta\"))\n",
    "\n",
    "# Renomear os cabeçalhos das sequências\n",
    "for record in records:\n",
    "    description_parts = record.description.split()\n",
    "    second_term = description_parts[1] if len(description_parts) > 1 else \"\"\n",
    "    new_description = f\"{second_term}\"\n",
    "    record.description = new_description\n",
    "    record.id = second_term  # Manter apenas o segundo termo como ID da sequência\n",
    "\n",
    "# Salvar as sequências com os novos cabeçalhos\n",
    "SeqIO.write(records, output_file, \"fasta\")\n",
    "\n",
    "print(f\"Sequências renomeadas salvas em: {output_file}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "três arquivos com as sequências prontas para fazer o alinhamento foram organizados:\n",
    "\n",
    "/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_renamed_second_term.fasta\n",
    "/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_renamed_second_term.fasta\n",
    "/home/nathan/Documents/Doutorado_diversidade_genética/Filogeografia/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_renamed_second_term.fasta\n",
    "\n",
    "será feito o alinhamento dessas sequências"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "outputhat23=2\n",
      "treein = 0\n",
      "compacttree = 0\n",
      "stacksize: 8192 kb\n",
      "generating a scoring matrix for nucleotide (dist=200) ... done\n",
      "All-to-all alignment.\n",
      "tbfast-pair (nuc) Version 7.490\n",
      "alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0\n",
      "0 thread(s)\n",
      "\n",
      "outputhat23=2\n",
      "Loading 'hat3.seed' ... \n",
      "done.\n",
      "Writing hat3 for iterative refinement\n",
      "generating a scoring matrix for nucleotide (dist=200) ... done\n",
      "Gap Penalty = -1.53, +0.00, +0.00\n",
      "tbutree = 1, compacttree = 0\n",
      "Constructing a UPGMA tree ... \n",
      "  100 / 104\n",
      "done.\n",
      "\n",
      "Progressive alignment ... \n",
      "STEP   103 /103 \n",
      "done.\n",
      "tbfast (nuc) Version 7.490\n",
      "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n",
      "1 thread(s)\n",
      "\n",
      "minimumweight = 0.000010\n",
      "autosubalignment = 0.000000\n",
      "nthread = 0\n",
      "randomseed = 0\n",
      "blosum 62 / kimura 200\n",
      "poffset = 0\n",
      "niter = 2\n",
      "sueff_global = 0.100000\n",
      "nadd = 2\n",
      "Loading 'hat3' ... done.\n",
      "generating a scoring matrix for nucleotide (dist=200) ... done\n",
      "\n",
      "  100 / 104\n",
      "Segment   1/  1    1- 709\n",
      "STEP 002-102-1  identical.    identical.    identical.    identical.    identical.    identical.    identical.    identical.   \n",
      "Converged.\n",
      "\n",
      "done\n",
      "dvtditr (nuc) Version 7.490\n",
      "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n",
      "0 thread(s)\n",
      "\n",
      "\n",
      "Strategy:\n",
      " L-INS-i (Probably most accurate, very slow)\n",
      " Iterative refinement method (<2) with LOCAL pairwise alignment information\n",
      "\n",
      "If unsure which option to use, try 'mafft --auto input > output'.\n",
      "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n",
      "\n",
      "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n",
      "It tends to insert more gaps into gap-rich regions than previous versions.\n",
      "To disable this change, add the --leavegappyregion option.\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Alinhamento concluído: /home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_aligned.fas\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "outputhat23=16\n",
      "treein = 0\n",
      "compacttree = 0\n",
      "stacksize: 8192 kb\n",
      "generating a scoring matrix for nucleotide (dist=200) ... done\n",
      "All-to-all alignment.\n",
      "tbfast-pair (nuc) Version 7.490\n",
      "alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0\n",
      "0 thread(s)\n",
      "\n",
      "outputhat23=16\n",
      "Loading 'hat3.seed' ... \n",
      "done.\n",
      "Writing hat3 for iterative refinement\n",
      "generating a scoring matrix for nucleotide (dist=200) ... done\n",
      "Gap Penalty = -1.53, +0.00, +0.00\n",
      "tbutree = 1, compacttree = 0\n",
      "Constructing a UPGMA tree ... \n",
      "   50 / 55\n",
      "done.\n",
      "\n",
      "Progressive alignment ... \n",
      "STEP    54 /54 \n",
      "done.\n",
      "tbfast (nuc) Version 7.490\n",
      "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n",
      "1 thread(s)\n",
      "\n",
      "minimumweight = 0.000010\n",
      "autosubalignment = 0.000000\n",
      "nthread = 0\n",
      "randomseed = 0\n",
      "blosum 62 / kimura 200\n",
      "poffset = 0\n",
      "niter = 16\n",
      "sueff_global = 0.100000\n",
      "nadd = 16\n",
      "Loading 'hat3' ... done.\n",
      "generating a scoring matrix for nucleotide (dist=200) ... done\n",
      "\n",
      "   50 / 55\n",
      "Segment   1/  1    1- 875\n",
      "STEP 002-053-1  identical.    identical.    identical.    identical.    identical.   \n",
      "Converged.\n",
      "\n",
      "done\n",
      "dvtditr (nuc) Version 7.490\n",
      "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n",
      "0 thread(s)\n",
      "\n",
      "\n",
      "Strategy:\n",
      " L-INS-i (Probably most accurate, very slow)\n",
      " Iterative refinement method (<16) with LOCAL pairwise alignment information\n",
      "\n",
      "If unsure which option to use, try 'mafft --auto input > output'.\n",
      "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n",
      "\n",
      "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n",
      "It tends to insert more gaps into gap-rich regions than previous versions.\n",
      "To disable this change, add the --leavegappyregion option.\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Alinhamento concluído: /home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_aligned.fas\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "outputhat23=2\n",
      "treein = 0\n",
      "compacttree = 0\n",
      "stacksize: 8192 kb\n",
      "generating a scoring matrix for nucleotide (dist=200) ... done\n",
      "All-to-all alignment.\n",
      "tbfast-pair (nuc) Version 7.490\n",
      "alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0\n",
      "0 thread(s)\n",
      "\n",
      "outputhat23=2\n",
      "Loading 'hat3.seed' ... \n",
      "done.\n",
      "Writing hat3 for iterative refinement\n",
      "generating a scoring matrix for nucleotide (dist=200) ... done\n",
      "Gap Penalty = -1.53, +0.00, +0.00\n",
      "tbutree = 1, compacttree = 0\n",
      "Constructing a UPGMA tree ... \n",
      "  100 / 104\n",
      "done.\n",
      "\n",
      "Progressive alignment ... \n",
      "STEP   103 /103 \n",
      "done.\n",
      "tbfast (nuc) Version 7.490\n",
      "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n",
      "1 thread(s)\n",
      "\n",
      "minimumweight = 0.000010\n",
      "autosubalignment = 0.000000\n",
      "nthread = 0\n",
      "randomseed = 0\n",
      "blosum 62 / kimura 200\n",
      "poffset = 0\n",
      "niter = 2\n",
      "sueff_global = 0.100000\n",
      "nadd = 2\n",
      "Loading 'hat3' ... done.\n",
      "generating a scoring matrix for nucleotide (dist=200) ... done\n",
      "\n",
      "  100 / 104\n",
      "Segment   1/  1    1- 667\n",
      "STEP 001-098-0  identical.    identical.    identical.    identical.    identical.    identical.   "
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Alinhamento concluído: /home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_aligned.fas\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "STEP 002-102-1  identical.   \n",
      "Converged.\n",
      "\n",
      "done\n",
      "dvtditr (nuc) Version 7.490\n",
      "alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0\n",
      "0 thread(s)\n",
      "\n",
      "\n",
      "Strategy:\n",
      " L-INS-i (Probably most accurate, very slow)\n",
      " Iterative refinement method (<2) with LOCAL pairwise alignment information\n",
      "\n",
      "If unsure which option to use, try 'mafft --auto input > output'.\n",
      "For more information, see 'mafft --help', 'mafft --man' and the mafft page.\n",
      "\n",
      "The default gap scoring scheme has been changed in version 7.110 (2013 Oct).\n",
      "It tends to insert more gaps into gap-rich regions than previous versions.\n",
      "To disable this change, add the --leavegappyregion option.\n",
      "\n"
     ]
    }
   ],
   "source": [
    "\n",
    "# Lista de arquivos de entrada e saída\n",
    "input_files = [\n",
    "    \"/home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_renamed_second_term.fasta\",\n",
    "    \"/home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_renamed_second_term.fasta\",\n",
    "    \"/home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_renamed_second_term.fasta\"\n",
    "]\n",
    "\n",
    "output_files = [\n",
    "    \"/home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_aligned.fas\",\n",
    "    \"/home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_aligned.fas\",\n",
    "    \"/home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_aligned.fas\"\n",
    "]\n",
    "\n",
    "# Alinhar sequências usando MAFFT e salvar no formato .fas \n",
    "for input_file, output_file in zip(input_files, output_files):\n",
    "    command = [\"mafft\", \"--auto\", input_file]\n",
    "    with open(output_file, \"w\") as output_handle:\n",
    "        subprocess.run(command, stdout=output_handle)\n",
    "    print(f\"Alinhamento concluído: {output_file}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Alinhamento do arquivo: /home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_aligned.fas\n",
      "Alignment with 104 rows and 708 columns\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BMD830\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BC767\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BC774\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att FC1402\n",
      "gttaaaccccctcctttactaattaacccgtatgccctatcaat...att SM1577\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att FC1065\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att TAP1480\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BC772\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BC728\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BMD840\n",
      "gttaaaccccctcctttactaattaacccgtatgccctatcaat...att SM1581\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BMD376\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att FC1404\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att FC1036\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BC775\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att TAP1483\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BMD375\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att AA936\n",
      "...\n",
      "gttaaaccccctcctttactaattaacccatatgccctatcaat...att BMD846\n",
      "\n",
      "\n",
      "Alinhamento do arquivo: /home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_aligned.fas\n",
      "Alignment with 55 rows and 874 columns\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa FC1015_2\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa BC726\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa SM1577\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa SM1580\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa AA925_2\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa SM1587\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa TAP1474_1\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa TAP1476\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa FC1038\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa AA936_1\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa AA936_2\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa SM1578\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa AA947_2\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa AA947_1\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa BC728\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa BC766\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa AA948\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa TAP1477_1\n",
      "...\n",
      "tggagaaagtggtgtcggaaaagctggcgtcctaccaggcttct...caa TAP1474_2\n",
      "\n",
      "\n",
      "Alinhamento do arquivo: /home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_aligned.fas\n",
      "Alignment with 104 rows and 666 columns\n",
      "tttggctccctcctagggacatgcctcattgtacaaattgttac...gac BMD826\n",
      "tttggctccctcctagggacatgccttattgtacaaattgttac...gac FC479\n",
      "tttggctccctcttaggaacatgccttattgtacaaattgttac...gac SM1580\n",
      "tttggctccctcctaggaacatgcctcattgtacaaattgttac...gac BC765\n",
      "tttggctccctcctagggacatgccttattgtacaaattgttac...gac TAP1521\n",
      "tttggctccctcctagggacatgccttattgtacaaattgttac...gac TAP1476\n",
      "tttggctccctcttaggaacatgccttattgtacaaattgttac...gac SM1586\n",
      "tttggctccctcctagggacatgcctcattgtacaaattgttac...gac BMD829\n",
      "tttggctccctcctagggacatgcctcattgtacaaattgttac...gac BMD830\n",
      "tttggctccctcctagggacatgcctcattgtacaaattgttac...gac FC1037\n",
      "tttggctccctcctagggacatgcctcattgtacaaattgttac...gac FC1404\n",
      "tttggctccctcctagggacatgcctcattgtacaaattgttac...gac BMD841\n",
      "tttggctccctcctaggaacatgcctcattgtacaaattgttac...gac BC730\n",
      "tttggctccctcctagggacatgcctcattgtacaaattgttac...gac BMD837\n",
      "tttggctccctcttaggaacatgccttattgtacaaattgttac...gac SM1588\n",
      "tttggctccctcctagggacatgccttattgtacaaattgttac...gac TAP1473\n",
      "tttggctccctcctagggacatgcctcattgtacaaattgttac...gac BMD828\n",
      "tttggctccctcctagggacatgcctcatcgtacaaattgttac...gac TAP1519\n",
      "...\n",
      "tttggctccctcctagggacatgcctcattgtacaaattgttac...gac FC1019\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "\n",
    "# Lista de arquivos de alinhamento\n",
    "alignment_files = [\n",
    "    \"/home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/ND2_Proceratophrys_boiei_aligned.fas\",\n",
    "    \"/home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU025551_EU025679_sequences/c-myc_Proceratophrys_boiei_aligned.fas\",\n",
    "    \"/home/nathan/Documents/Doutorado_diversidade_genética/Phylogeogra/EU017577_EU018044_sequences/cytb_Proceratophrys_boiei_aligned.fas\"\n",
    "]\n",
    "\n",
    "# Visualizar os alinhamentos\n",
    "for alignment_file in alignment_files:\n",
    "    alignment = AlignIO.read(alignment_file, \"fasta\")\n",
    "    print(f\"Alinhamento do arquivo: {alignment_file}\")\n",
    "    print(alignment)\n",
    "    print(\"\\n\")"
   ]
  }
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