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Summary

Bio::Index::Fastq - Interface for indexing (multiple) fastq files

Package variables

Included modules

Inherit

Bio::Index::AbstractSeq

Synopsis

    # Complete code for making an index for several
    # fastq files
    use Bio::Index::Fastq;
    use strict;

    my $Index_File_Name = shift;
    my $inx = Bio::Index::Fastq->new(
        '-filename' => $Index_File_Name,
        '-write_flag' => 1);
    $inx->make_index(@ARGV);

    # Print out several sequences present in the index
    # in Fastq format
    use Bio::Index::Fastq;
    use strict;

    my $Index_File_Name = shift;
    my $inx = Bio::Index::Fastq->new('-filename' => $Index_File_Name);
    my $out = Bio::SeqIO->new('-format' => 'Fastq','-fh' => \*STDOUT);

    foreach my $id (@ARGV) {
        my $seq = $inx->fetch($id); # Returns Bio::Seq::SeqWithQuality object
	$out->write_seq($seq);
    }

    # or, alternatively

    my $seq = $inx->get_Seq_by_id($id); #identical to fetch

Description

Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
and provides the basic funtionallity for indexing fastq files, and
retrieving the sequence from them. Note: for best results 'use strict'.
Bio::Index::Fastq supports the Bio::DB::BioSeqI interface, meaning
it can be used as a Sequence database for other parts of bioperl

Methods

Methods description

 Title   : _file_format
 Function: The file format for this package, which is needed
           by the SeqIO system when reading the sequence.
 Returns : 'Fastq'

  Title   : _index_file
  Usage   : $index->_index_file( $file_name, $i )
  Function: Specialist function to index FASTQ format files.
            Is provided with a filename and an integer
            by make_index in its SUPER class.
  Example : 
  Returns : 
  Args    :

  Title   : default_id_parser
  Usage   : $id = default_id_parser( $header )
  Function: The default Fastq ID parser for Fastq.pm
            Returns $1 from applying the regexp /^>\s*(\S+)/
            to $header.
  Returns : ID string
  Args    : a fastq header line string

  Title   : id_parser
  Usage   : $index->id_parser( CODE )
  Function: Stores or returns the code used by record_id to
            parse the ID for record from a string.  Useful
            for (for instance) specifying a different
            parser for different flavours of FASTQ file. 
            Returns \&default_id_parser (see below) if not
            set. If you supply your own id_parser
            subroutine, then it should expect a fastq
            description line.  An entry will be added to
            the index for each string in the list returned.
  Example : $index->id_parser( \&my_id_parser )
  Returns : ref to CODE if called without arguments
  Args    : CODE

Methods code

BEGIN {

     $VERSION = 0.2;

}

sub _file_format {

    return 'Fastq';

}

sub _index_file {

    my( $self,
        $file, # File name
        $i,    # Index-number of file being indexed
        ) = @_;
    
    my( $begin,     # Offset from start of file of the start
                    # of the last found record.
        );

    $begin = 0;

    my $id_parser = $self->id_parser;
	my $c = 0;
    open FASTQ, $file or $self->throw("Can't open file for read : $file");
    # Main indexing loop
    while (<FASTQ>) {
        if (/^@/) {
            # $begin is the position of the first character after the '@'
            my $begin = tell(FASTQ) - length( $_ ) + 1;
            foreach my $id (&$id_parser($_)) {
                $self->add_record($id, $i, $begin);
		$c++;
            }
        }
    }

    close FASTQ;
    return ($c);

}

sub _version {

    return $VERSION;

}

sub default_id_parser {

        if ($_[0] =~ /^@\s*(\S+)/) {
        return $1;
    } else {
        return;
    }
}

1;

}

sub id_parser {

    my( $self, $code ) = @_;
    
    if ($code) {
        $self->{'_id_parser'} = $code;
    }
    return $self->{'_id_parser'} ||\& default_id_parser;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org             - General discussion
  http://bioperl.org/MailList.shtml - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email - avc@sanger.ac.uk

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _