GJ-utilities

Overview:

GJutilities is a collection of scripts useful in the analysis and management of:

• Initial sequencing data from Illumina high throughput NGS machines
• Wrappers for running and parsing commonly used command line tools like bedtools, samtools etc.
• Various data visualization techniques

Table of contents

1. An empty template for a python script
2. Merge Illumina Samples
3. Combined Volcano Plots

Description

For various scripts:

1. gjain_python_script_template.py

   [gjain@gjvbx GJutilities ] $ python gjain_python_script_template.py 
   
   ***********************************************
   - PROGRAM: gjain_python_script_template.py
   - CONTACT: Gaurav Jain ([email protected])
   - LICENSE: Copyright (C) <year>  <name of author>
   	   This program is free software: you can redistribute it and/or modify  
   	   it under the terms of the GNU General Public License as published by
   	   the Free Software Foundation, either version 3 of the License, or
   	   (at your option) any later version.
   
   	   This program is distributed in the hope that it will be useful,
   	   but WITHOUT ANY WARRANTY; without even the implied warranty of
   	   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   	   GNU General Public License for more details.
   
   	   You should have received a copy of the GNU General Public License
   	   along with this program.  If not, see <http://www.gnu.org/licenses/>.
   ***********************************************
   
   usage: gjain_python_script_template.py [-h] -a1 --myarg1 [-a2 --myarg2] [-a3 --myarg3] [-fg] [-a4 {n,r,c}]
   
   optional arguments:
   -h, --help            show this help message and exit
   -a1 --myarg1          *My argument one
   -a2 --myarg2          My argument two
   -a3 --myarg3          My argument three
   -fg, --smflag         This is some flag. if set, perform some additional tasks
   -a4 {n,r,c}, --selval {n,r,c}
   		      The argument that can have only certain options -
   		      Please enter: 
   				-sc='n' for NONE
   				-sc='r' for ROW
   				-sc='c' for COLUMN
   
   ----------------- SAMPLE USAGE ------------------
   - python gjain_python_script_template.py -a1="my_first_argument" 
   - python gjain_python_script_template.py -a1="my_first_argument" -a2="my_second_argument" -a3=49
   - python gjain_python_script_template.py -a1="my_first_argument" -a2="my_second_argument" -a3=49 -fg
   - python gjain_python_script_template.py -a1="my_first_argument" -a2="my_second_argument" -a3=49 -fg -a4='r'
   

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2. merge_illumina_samples.py

   [gjain@gjvbx GJutilities ] $ python merge_illumina_samples.py 
   
   ***********************************************
   - PROGRAM: merge_illumina_samples.py
   - CONTACT: Gaurav Jain([email protected])
   ***********************************************
   
   usage: merge_illumina_samples.py [-h] -id --indir -od --otdir [-du]
   
   optional arguments:
   -h, --help    show this help message and exit
   -id --indir   *Input directory containing the unmerged fastQ files
   -od --otdir   *Output directory to save the merged fastQ files
   -du, --dudir  if set, delete unmerged fastq files dir 
   				(Default: False)
   
   ----------------- SAMPLE USAGE ------------------
   - python scripts/merge_illumina_samples.py -id=input/raw_fastq/unmerged -od=input/raw_fastq/merged
   - python scripts/merge_illumina_samples.py -id=input/raw_fastq/unmerged -od=input/raw_fastq/merged -du
   -------------------------------------------------
   CONTACT: 
   	Gaurav Jain
   	[email protected]
   -------------------------------------------------
   

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3. draw_volcano_plots.py

   [gjain@gjvbx GJutilities ] $ python draw_combined_volcano_plots.py 
   
   ***********************************************
   - PROGRAM: draw_volcano_plots.py
   - CONTACT: Gaurav Jain([email protected])
   ***********************************************
   
   usage: draw_combined_volcano_plots.py [-h] -af --inpfl1 -bf --inpfl2 -of
   									--opfile [-ix --idxnme] [-nf]
   
   optional arguments:
   -h, --help              Show this help message and exit
   -af --inpfl1          * Input data file1. Ex: deseq2 results file1
   -bf --inpfl2          * Input data file2. Ex: deseq2 results file2
   -of --opfile          * Output file name
   -ix --idxnme            Index column name
   			- (Default = GeneName)
   -nf, --filter_smallrna
   			if set, filter any feature (based on low expression) from the  inputDF
   			(Default = False)
   
   ----------------- SAMPLE USAGE ------------------
   - python draw_combined_volcano_plots.py -af=results_DEseq2/A_over_C_DE_RESULTS_common_gene_names.txt -bf=results_DEseq2/B_over_D_DE_RESULTS_common_gene_names.txt -of=diagnosis_plots/A_over_C_combined_with_B_over_D_volcano_plots.txt -ix=GeneName
   -------------------------------------------------
   CONTACT: 
   	Gaurav Jain
   	[email protected]
   -------------------------------------------------
   

   • Example output plot

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