https://github.com/mkviatkovskii/bioutils

Collection of bioinformatics-related tools written in Python
https://github.com/mkviatkovskii/bioutils

bioinformatics biopython genome-analysis

Last synced: 9 months ago
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Collection of bioinformatics-related tools written in Python

• Host: GitHub
• URL: https://github.com/mkviatkovskii/bioutils
• Owner: mkviatkovskii
• License: mit
• Created: 2022-04-12T12:51:57.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2022-04-12T13:20:15.000Z (over 3 years ago)
• Last Synced: 2025-03-11T10:15:26.149Z (9 months ago)
• Topics: bioinformatics, biopython, genome-analysis
• Language: Python
• Homepage:
• Size: 4.88 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

          
# Longest gene search tool

## Summary

Tool for finding list of gene-like sequences of max common length for

given input list of sequences (aligned contigs). Input is in FASTA

format, output is in FASTA-2 format.

## Requirements

* Python 3.6+

* BioPython 1.71+

## Parameters

* `-i`, `--input-file`: input FASTA file with aligned contigs.

* `-o`, `--output-file`: path to output FASTA-2 file.

* `-ms`, `--min-similarity`: Minimal allowed similarity of sequences,

in [0, 1] interval. By default is 0.95.

## Example

```bash

python3 ./longest_gene.py -i examples/gregalis.fa -o output.fa

```