NAME

FASTX::PE - A Paired-End FASTQ files reader, based on FASTX::Reader.

VERSION

version 1.5.0

SYNOPSIS

  use FASTX::PE;
  my $filepath = '/path/to/assembly_R1.fastq';
  # Will automatically open "assembly_R2.fastq"
  my $fq_reader = FASTX::Reader->new({
    filename => "$filepath",
  });

  while (my $seq = $fasta_reader->getRead() ) {
    print $seq->{name}, "\t", $seq->{seq1}, "\t", $seq->{qual1}, "\n";
    print $seq->{name}, "\t", $seq->{seq2}, "\t", $seq->{qual2}, "\n";
  }

METHODS

new()

Initialize a new FASTX::Reader object passing 'filename' argument for the first pairend, and optionally 'rev' for the second (otherwise can be guessed substituting 'R1' with 'R2' and '_1.' with '_2.')

  my $pairend = FASTX::Reader->new({
      filename => "$file_R1",
      rev      => "$file_R2"
  });

To read from STDIN either pass {{STDIN}} as filename, or don't pass a filename at all. In this case the module will expect an interleaved pairedend file.

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

If a '_R2' file is not found, the module will try parsing as interleaved. This can be forced with:

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

getReads()

Will return the next sequences in the FASTA / FASTQ file. The returned object has these attributes:

name

header of the sequence (identifier)

comment1 and comment2

any string after the first whitespace in the header, for the first and second paired read respectively.

seq1 and seq2

DNA sequence for the first and the second pair, respectively

qual1 and qual2

quality for the first and the second pair, respectively

SEE ALSO

FASTX::Reader

The FASTA/FASTQ parser this module is based on.

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