Bioinformatic utils

This repository contains some scripts that could be useful for bioinformatics analysis.

Dependencies

• Python3.8 or superior;
• Libraries present in the requirements file.

Installation

After install the external programs, download the repository:

git clone https://github.com/Nickolaz47/bioinfo_utils.git 

Enter the folder and install the python libraries:

pip install -r requirements.txt

Scripts

Sequence validator

This script aims to remove nucleotide/aminoacid sequences that have some invalid character.

Usage

python3 sequence_validator.py -fi fasta input -fo fasta output -m (n or p)

Parameters

• fi: Fasta file input.
• fo: Fasta file output.
• m: Mode to run the script, n for nucleotide sequences and p for protein sequences.

Transcript filter

This script aims to generate a fasta file with only the longest transcript of each gene.

Usage

python3 transcript_filter.py -fi fasta input -fo fasta output -tp pattern

Parameters

• fi: Fasta file input.
• fo: Fasta file output.
• tp: Transcript pattern used to identify a transcript from a gene. Example: gene1-transc1, transcript pattern = "-".