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SeqExtractor is a script for extracting sequences from a FASTA file based on a list of sequence IDs provided in a separate file.

Prerequisites

  • Python 3
  • Biopython library (pip install biopython)

Installation

  1. Clone the repository:
git clone https://github.com/cavalheiromf10/SeqExtractor.git
cd SeqExtractor
  1. Make the script executable
foo@bar: ~$ chmod +x SeqExtractor.py

Usage

./SeqExtractor.py -i input_file -s sequence_file -o output_file

Arguments

input_file: File with one sequence ID per line.
sequence_file: FASTA file containing sequences to extract.
output_file: Name of the output file to save the extracted sequences.

Example

./SeqExtractor.py -i IDs_DUFs.txt -s Esalsugineum_173_v1.0.protein.fa -o output.fasta

This example will extract sequences from Esalsugineum_173_v1.0.protein.fa based on the sequence IDs listed in IDs_DUFs.txt and save the results to output.fasta.

Troubleshooting

If you encounter any issues with file permissions or missing files, check the error messages provided by the script. Ensure that Biopython is installed (pip install biopython).