Raw content of Bio::Index::Fastq # # # BioPerl module for Bio::Index::Fastq # # Cared for by Tony Cox <avc@sanger.ac.uk> # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Index::Fastq - Interface for indexing (multiple) fastq files =head1 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 =head1 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 =head1 FEED_BACK =head2 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 =head2 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://bugzilla.bioperl.org/ =head1 AUTHOR - Tony Cox Email - avc@sanger.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Index::Fastq; use vars qw($VERSION @ISA); use strict; use Bio::Index::AbstractSeq; use Bio::Seq; @ISA = qw(Bio::Index::AbstractSeq); # # Suggested fix by Michael G Schwern <schwern@pobox.com> to # get around a clash with CPAN shell... # BEGIN { $VERSION = 0.2; } sub _version { return $VERSION; } =head2 _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' =cut sub _file_format { return 'Fastq'; } =head2 _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 : =cut 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); } =head2 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 =cut sub id_parser { my( $self, $code ) = @_; if ($code) { $self->{'_id_parser'} = $code; } return $self->{'_id_parser'} || \&default_id_parser; } =head2 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 $header. Returns : ID string Args : a fastq header line string =cut sub default_id_parser { if ($_[0] =~ /^@\s*(\S+)/) { return $1; } else { return; } } 1;