metagomics / fasta-trimmer

Program to remove sequences from FASTA file with no matching peptides.

fasta-trimmer

FASTA trimmer takes in a FASTA file and a list of unmodified peptide sequences and outputs text for a new FASTA file where all protein entries for which no peptide could be matched are removed.

Because FASTA files can be very large, the FASTA files is processed 1,000 sequences at a time. You will notice this in the screen output as the program is running.

How to run:

Ensure Java is installed on your system: https://java.com/en/download/

Download the latest release: https://github.com/metagomics/fasta-trimmer/releases

Run with: java -jar fastaTrimmer.jar /path/to/file.fasta /path/to/peptide.list >/path/to/new/file.fasta

Usage:

java -jar fastaTrimmer.jar /path/to/file.fasta /path/to/peptide.list >/path/to/new/file.fasta

"peptide.list" should be a list of unmodified peptide sequences, one per line.

Alternatively, "peptide.list" may be a tab-delimited file, so long as the peptide sequence is the first column.