Analysis of Large Blast Inputs: A.L.B.I

This package is a collection of individual python scripts that can perform data parsing of standalone BLAST+ ouput file. Besides this, SLURM and PBS scripts have been provided to run large BLAST+ inputs which can be useful for metagenomic data analysis.

Installation

Does not require installation, can be run by invoking python in windows or linux. All the scripts were written in Python v.3.8.0

Prerequisites

python library: numpy & matplotlib

Usage

For extracting the top similarity hits out of the BLAST+ default 5:

python topscore_headers.py

Input file: blast_input.txt

Output file: out2.txt

For finding relative abundance of a single user defined protien

python relative_abundance.py

Input file: out2.txt

refer Figure_1.png

For comparing abundance of multiple user defined proteins with graphical output

python protein_graph.py

Input file: out2.txt

refer Figure_2.png

To convert BLAST+ output file into FASTA file

Keeping im mind the various requirements a user may have, this script is divided into 3 segments where the user can retrieve the information required. ALthough, the entire script can work independantluy as well.

python blast2fasta.py

Input file: blast_input.txt

Output file: Fasta.txt

HPC job scripts

Make the necessary changes such as the no. of CPUs, threads according to your configuration. Save the file with .slurm, .sh extensions and adjust line breaking styles based on your system requirements.

Support

SRM-IST HPC systems

License

GNU General Public License v3.0 (https://www.gnu.org/licenses/gpl-3.0.en.html)

Project status

Work presented at ICIBLS 2020. "Proceedings of International Conference on Innovations in Biotechnology and Life" (AB-005) I S B N : 978-93-88647-32-8; D O I : 10.6084/m9.figshare.13947833