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

avvypaks/GenGrab