FASTX::XS

NAME

FASTX::XS - Fast FASTA/FASTQ parser using kseq.h

SYNOPSIS

use FASTX::XS;

# Parse a FASTA or FASTQ file (can be gzipped)
my $parser = FASTX::XS->new("sequence.fa.gz");

# Iterate through all sequences
while (my $seq = $parser->next_seq()) {
    print "Name: $seq->{name}\n";
    print "Sequence: $seq->{seq}\n";
    
    # Print comment if available
    print "Comment: $seq->{comment}\n" if exists $seq->{comment};
    
    # Print quality if available (FASTQ)
    print "Quality: $seq->{qual}\n" if exists $seq->{qual};
}

DESCRIPTION

FASTX::XS is a Perl module for fast parsing of FASTA and FASTQ files using the kseq.h library from Heng Li's klib. It supports both uncompressed and gzipped files.

This module provides a simple interface to access sequences from FASTA/FASTQ files with high performance and low memory usage.

METHODS

new(filename)

Creates a new parser object for the specified file. The file can be either a regular FASTA/FASTQ file or a gzipped file (.gz extension).

next_seq()

Returns the next sequence from the file as a hash reference with the following keys:

• name - The sequence identifier (required)
• seq - The sequence string (required)
• comment - The comment string (optional)
• qual - The quality string for FASTQ files (optional)

Returns undef when there are no more sequences to read.

AUTHOR

Andrea Telatin, proch@cpan.org

COPYRIGHT AND LICENSE

Copyright (C) 2025 by Quadram Institute Bioscience, Norwich, UK

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.