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Author image Andrea Telatin 🧬
and 1 contributors

NAME

FASTX::Reader - A simple module to parse FASTA and FASTQ files, supporting compressed files and paired-ends.

VERSION

version 1.0.5

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() ) {
    f $seq->{name}, "\t", $seq->{seq}, "\t", $seq->{qual}, "\n";
  }

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METHODS

new()

Initialize a new FASTX::Reader object passing 'filename' argument. Will open a filehandle stored as $object->{fh}.

  my $seq_from_file = FASTX::Reader->new({ filename => "$file" });

To read from STDIN either pass {{STDIN}} as filename, or don't pass a filename at all:

  my $seq_from_stdin = FASTX::Reader->new();

The parameter loadseqs will preload all sequences in a hash having the sequence name as key and its sequence as value.

  my $seq_from_file = FASTX::Reader->new({
    filename => "$file",
    loadseqs => 1,
  });

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 simpler, FASTQ-specific, parser. Attributes of the returned object are name, comment, seq, qual (as for getRead()). It will alter the status attribute of the reader object if the FASTQ format looks terribly wrong.

  use FASTX::Reader;
  my $filepath = '/path/to/assembly.fastq';
  my $fasta_reader = FASTX::Reader->new({ filename => "$filepath" });

  while (my $seq = $fasta_reader->getFastqRead() ) {
    die "Error parsing $filepath: " . $fasta_reader->{message} if ($fasta_reader->{status} != 1);
    print $seq->{name}, "\t", $seq->{seq}, "\t", $seq->{qual}, "\n";
  }

getIlluminaRead()

If the file is FASTQ, this method returns the same read object as getRead() but with a simpler parser. Attributes of the returned object are name, comment, seq, qual (as for getRead()). In addition to this it will parse the name and comment populating these properties fromt the read name: instrument, run, flowcell, lane, tile, x, y, umi.

If the comment is also present the following will also populated: read (1 for R1, and 2 for R2), index (barcode of the current read), paired_index (barcode of the other read) and filtered (true if the read is to be discarded, false elsewhere).

It will alter the status attribute of the reader object if the FASTQ format looks terribly wrong.

  while (my $seq = $fasta_reader->getIlluminaRead() ) {
    print $seq->{name}, "\t", $seq->{instrument}, ',', $seq->{index1}, "\n";
  }

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 module is a has been inspired by the readfq() subroutine originally written by Heng Li, that I updated to retain sequence comments. See: readfq repository

Fabrizio Levorin

has contributed to the prototyping of this module

SEE ALSO

BioX::Seq::Stream

The module I would have used if it was available when I started working on this. The .gz reader implementation comes from this module.

AUTHOR

Andrea Telatin <andrea@telatin.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2019 by Andrea Telatin.

This is free software, licensed under:

  The MIT (X11) License