Raw content of Bio::SeqIO::phd # $Id: phd.pm,v 1.17 2002/12/09 23:50:23 matsallac Exp $ # # Copyright (c) 1997-2001 bioperl, Chad Matsalla. All Rights Reserved. # This module is free software; you can redistribute it and/or # modify it under the same terms as Perl itself. # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::phd - .phd file input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L<Bio::SeqIO> class. =head1 DESCRIPTION This object can transform .phd files (from Phil Green's phred basecaller) to and from Bio::Seq::SeqWithQuality objects =head1 FEEDBACK =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://www.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 Chad Matsalla Chad Matsalla bioinformatics@dieselwurks.com =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org =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::SeqIO::phd; use vars qw(@ISA); use strict; use Bio::SeqIO; use Bio::Seq::SeqFactory; @ISA = qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); if( ! defined $self->sequence_factory ) { $self->sequence_factory(new Bio::Seq::SeqFactory (-verbose => $self->verbose(), -type => 'Bio::Seq::SeqWithQuality')); } } =head2 next_seq() Title : next_seq() Usage : $swq = $stream->next_seq() Function: returns the next phred sequence in the stream Returns : Bio::Seq::SeqWithQuality object Args : NONE Notes : This is really redundant because AFAIK there is no such thing as a .phd file that contains more then one sequence. It is included as an interface thing and for consistency. =cut sub next_seq { my ($self,@args) = @_; my ($entry,$done,$qual,$seq); my ($id,@lines, @bases, @qualities) = (''); if (!($entry = $self->_readline)) { return; } if ($entry =~ /^BEGIN_SEQUENCE\s+(\S+)/) { $id = $1; } my $in_dna = 0; my $base_number = 0; while ($entry = $self->_readline) { return if (!$entry); chomp($entry); if ($entry =~ /^BEGIN_CHROMAT:\s+(\S+)/) { # this is where I used to grab the ID if (!$id) { $id = $1; } $entry = $self->_readline(); } if ($entry =~ /^BEGIN_DNA/) { $entry =~ /^BEGIN_DNA/; $in_dna = 1; $entry = $self->_readline(); } if ($entry =~ /^END_DNA/) { $in_dna = 0; } if ($entry =~ /^END_SEQUENCE/) { } if (!$in_dna) { next; } $entry =~ /(\S+)\s+(\S+)/; push @bases,$1; push @qualities,$2; push(@lines,$entry); } # $self->debug("csmCreating objects with id = $id\n"); my $swq = $self->sequence_factory->create (-seq => join('',@bases), -qual => \@qualities, -id => $id, -primary_id => $id, -display_id => $id, ); return $swq; } =head2 write_seq Title : write_seq(-SeqWithQuality => $swq, <comments>) Usage : $obj->write_seq( -SeqWithQuality => $swq,); Function: Write out an scf. Returns : Nothing. Args : Requires: a reference to a SeqWithQuality object to form the basis for the scf. Any other arguments are assumed to be comments and are put into the comments section of the scf. Read the specifications for scf to decide what might be good to put in here. Notes : These are the comments that reside in the header of a phd file at the present time. If not provided in the parameter list for write_phd(), the following default values will be used: CHROMAT_FILE: $swq->id() ABI_THUMBPRINT: 0 PHRED_VERSION: 0.980904.e CALL_METHOD: phred QUALITY_LEVELS: 99 TIME: <current time> TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: unknown CHEM: unknown DYE: unknown IMPORTANT: This method does not write the trace index where this call was made. All base calls are placed at index 1. =cut sub write_seq { my ($self,@args) = @_; my @phredstack; my ($label,$arg); my ($swq, $chromatfile, $abithumb, $phredversion, $callmethod, $qualitylevels,$time, $trace_min_index, $trace_max_index, $chem, $dye ) = $self->_rearrange([qw(SEQWITHQUALITY CHROMAT_FILE ABI_THUMBPRINT PHRED_VERSION CALL_METHOD QUALITY_LEVELS TIME TRACE_ARRAY_MIN_INDEX TRACE_ARRAY_MAX_INDEX CHEM DYE )], @args); unless (ref($swq) eq "Bio::Seq::SeqWithQuality") { $self->throw("You must pass a Bio::Seq::SeqWithQuality object to write_scf as a parameter named \"SeqWithQuality\""); } my $id = $swq->id(); if (!$id) { $id = "UNDEFINED in SeqWithQuality Object"; } push @phredstack,("BEGIN_SEQUENCE $id","","BEGIN_COMMENT",""); $chromatfile = 'undefined in write_phd' unless defined $chromatfile; push @phredstack,"CHROMAT_FILE: $chromatfile"; $abithumb = 0 unless defined $abithumb; push @phredstack,"ABI_THUMBPRINT: $abithumb"; $phredversion = "0.980904.e" unless defined $phredversion; push @phredstack,"PHRED_VERSION: $phredversion"; $callmethod = 'phred' unless defined $callmethod; push @phredstack,"CALL_METHOD: $callmethod"; $qualitylevels = 99 unless defined $qualitylevels; push @phredstack,"QUALITY_LEVELS: $qualitylevels"; $time = localtime() unless defined $time; push @phredstack,"TIME: $time"; $trace_min_index = 0 unless defined $trace_min_index; push @phredstack,"TRACE_ARRAY_MIN_INDEX: $trace_min_index"; $trace_max_index = '10000' unless defined $trace_max_index; push @phredstack,"TRACE_ARRAY_MAX_INDEX: $trace_max_index"; $chem = 'unknown' unless defined $chem; push @phredstack,"CHEM: $chem"; $dye = 'unknown' unless defined $dye; push @phredstack, "DYE: $dye"; push @phredstack,("END_COMMENT","","BEGIN_DNA"); foreach (@phredstack) { $self->_print($_."\n"); } my $length = $swq->length(); if ($length eq "DIFFERENT") { $self->throw("Can't create the phd because the sequence and the quality in the SeqWithQuality object are of different lengths."); } for (my $curr = 1; $curr<=$length; $curr++) { $self->_print (uc($swq->baseat($curr))." ". $swq->qualat($curr)." 10". "\n"); } $self->_print ("END_DNA\n\nEND_SEQUENCE\n"); $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1; __END__