https://github.com/benhg/isolate-single-gene

Isolate a single gene from genetic data.
https://github.com/benhg/isolate-single-gene

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Isolate a single gene from genetic data.

• Host: GitHub
• URL: https://github.com/benhg/isolate-single-gene
• Owner: benhg
• Created: 2020-04-20T18:23:54.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2020-04-21T17:58:24.000Z (almost 5 years ago)
• Last Synced: 2024-11-01T22:42:58.756Z (3 months ago)
• Language: Python
• Size: 382 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# GFF Feature Extractor

## Introduction and Motivation

Looking around, it was surprisingly difficult to find a simple script for extracting features specified with a GFFv3 file. This is meant to be a dead-simple implementation of a CLI tool for extracting features from a database.

## Description

Given a FASTA formatted database of sequences and a GFFv3 file which contains features and their locations within sequences contained in the FASTA formatted database, this will extract the features and put them into a new FASTA file, with each entry titled the same way as the input, plus the name of the feature which was extracted. Here's an example. 

Input file:

```

>seq1

ACAGACTGCCGGTGATAAGCCGGAGGAAGGTGAGGATGACGTCAAGTCATCATGCCCCTTATGCCCTGGGCGACACACGTGCTACAATGGCCGGGACAAAGGGTCGCGATCCCGCGAGGGTGAGCTAACCCCAAAAACCCGTCCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGCCGGAATCGCTAGTAATCGCCGGTCAGCCATACGGCGGTGAATTCGTTCCCGGGCCTTGTACACACCGCCCGTCACACTATGGGAGCTGGCCATGCCCGAAGTCGTTACCTTAACCGCAAGGAGGGGGATGCCGAAGGCAGGGCTAGTGACTGGAGTGAAGTCGTAACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCA

>seq2

ACAGACTGCCGGTGATAAGCCGGAGGAAGGTGAGGATGACGTCAAGTCATCATGCCCCTTATGCCCTGGGCGACACACGTGCTACAATGGCCGGGACAAAGGGTCGCGATCCCGCGAGGGTGAGCTAACCCCAAAAACCCGTCCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGCCGGAATCGCTAGTAATCGCCGGTCAGCCATACGGCGGTGAATTCGTTCCCGGGCCTTGTACACACCGCCCGTCACACTATGGGAGCTGGCCATGCCCGAAGTCGTTACCTTAACCGCAAGGAGGGGGATGCCGAAGGCAGGGCTAGTGACTGGAGTGAAGTCGTAACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATCA

```

Output File:

```

>seq1,18S_rRNA

GGGTCGCGATCCCGCGAGGGTGAGCTAACCC

>seq2,28S_rRNA

TAGTGACTGGAGTGAAGTCGTAACAAGGTAGCCGTA

```

## Usage

Simple, command-line based usage:

```

usage: gff_biopy.py [-h] --locations LOCATIONS --db DB --out OUT

                    [--filter FILTER]

required arguments:

  --locations LOCATIONS

                        Path to locations file in GFF3 format

  --db DB               Path to database file in FASTA format

  --out OUT             Path to output file in FASTA format (needs not exist)

optional arguments:

  -h, --help            show this help message and exit

  --filter FILTER       Name of type of feature to extract. Stored as a name

                        in the qualifiers section. Example: '18S_rRNA'

```