NAME
FASTX::Reader - A lightweight FASTA and FASTQ reader based on Heng Li's parser.
VERSION
version 0.05
SYNOPSIS
use FASTX::Reader;
my $filepath = '/path/to/assembly.fastq';
die "Input file not found: $filepath\n" unless (-e "$filepath");
my $fasta_reader = FASTX::Reader->new({ filename => "$filepath" });
while (my $seq = $fasta_reader->getRead() ) {
print $seq->{name}, "\t", $seq->{seq}, "\t", $seq->{qual}, "\n";
}NAME
FASTX::Reader - a lightweight module to parse FASTA and FASTQ files, using Heng Li's readfq() method https://github.com/lh3/readfq, packaged in an object oriented parser.
METHODS
new()
Initialize a new FASTX::Reader object passing 'filename' argument. Will open a filehandle stored as $object->{fh}.
my $seq_from_file = FASTX::Reader->({ filename => "$file" });To read from STDIN either pass {{STDIN}} as filename, or don't pass a filename at all:
my $seq_from_stdin = FASTX::Reader->();getRead()
Will return the next sequence in the FASTA / FASTQ file using Heng Li's implementation of the readfq() algorithm. The returned object has these attributes:
- name
-
header of the sequence (identifier)
- comment
-
any string after the first whitespace in the header
- seq
-
actual sequence
- qual
-
quality if the file is FASTQ
getFastqRead()
If the file is FASTQ, this method returns the same read object as getRead() but with a faster parser. Attributes of the returned object are name, comment, seq, qual (as for getRead()).
getFileFormat(filename)
This subroutine returns 'fasta', 'fastq' or <undef> for a given filepath (this is not a method of the instantiated object)
ACKNOWLEDGEMENTS
- Heng Li's readfq()
-
This mnodule is a wrapper around the readfq() subroutine originally written by Heng Li, that I adapted to retain sequence comments.
See: readfq repository
CONTRIBUTORS
- Fabrizio Levorin
-
has substantially contributed to the development of this module, and is a collaborator in the GitHub repository
AUTHOR
Andrea Telatin <andrea.telatin@quadram.ac.uk>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2019 by Andrea Telatin.
This is free software, licensed under:
The MIT (X11) License