Ewan Birney


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


    # 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);

    # 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

    # or, alternatively

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


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


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AUTHOR - Tony Cox

Email - avc@sanger.ac.uk


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


 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   : 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


  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