Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

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

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::Quality object
               $out->write_seq($seq);
           }

           # or, alternatively
           my $id;
           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

FEED_BACK

   Mailing Lists
       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/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

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

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Tony Cox

       Email - avc@sanger.ac.uk

APPENDIX

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

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

   _index_file
         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    :

   id_parser
         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

   default_id_parser
         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