GenGrab

The is a bioinformatic tool to extract required gene segments from the entire genome according to defined gene boundary and for genome dataset preparation

Description

The package has two modules:

• Gene Extraction Module: The data results of gene boundaries from various softwares like ORF finder, Mitos can be executed in user defined format to extract required genes from all kinds of genomes (linear/circular and postive/negative stranded) by this module of GenGrab.
• Gene Separation Module: This module helps in preparing genome datasets of a single gene from a number of species.

Getting started

Installation

• The simplest way to set this up is to install the Anaconda Python distribution
• Otherwise, install the following dependencies: 1. pandas 2. tkinter 3. numpy

Running the program

GENE EXTRACTION MODULE:

• Unzip the program folder

• Open Anaconda Prompt

• Type “python“ followed by a space

• Drag and drop the “gengrab1.py” file (which is in the folder you just unzipped) onto the command prompt.

       `python “<gengrab1.py>”`
  

• Hit enter

• Give the genome sequence (test_genome.fas) from the dialog box just opened

• Give the gene boundaries in the required format(test_gene_boundary.csv) to run the program

• Save the output file in required path in .csv format from the dialog box

GENE SEPARATION MODULE:

Add all the annotated gene resuts in a single csv file to prepare the "gene separation file"

• Type python followed by a space in Anaconda Prompt

• Drag and drop the “gengrab2.py” file on the command prompt to run the program

     `python "<gengrab2.py>"` 
  

• Give the gene separation file (test_gene_separation.csv) from the dialog box

• Enter the gene name you want to filter

• Hit enter to run the code

• Save the output file in your required path

Feedback to contributors

• Goirik Dasgupta @goirikdg
• Avas Pakrashi @avvypaks

Acknowledgments

• Code used : https://codereview.stackexchange.com/questions/151329/reverse-complement-of-a-dna-string/151333