Ewan Birney

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;

    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;

    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.

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/MailList.shtml - About the mailing lists

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 email or the web:

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

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