Raw content of Bio::Assembly::IO::ace # $Id: ace.pm,v 1.1 2002/11/04 14:38:14 heikki Exp $ # ## BioPerl module for Bio::Assembly::IO::ace # # Copyright by Robson F. de Souza # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Assembly::IO::ace - module to load phrap ACE files. =head1 SYNOPSYS # Building an input stream use Bio::Assembly::IO; # Assembly loading methods $io = new Bio::Assembly::IO(-file=>"SGC0-424.fasta.screen.ace.1", -format=>"ace"); $assembly = $io->next_assembly; =head1 DESCRIPTION This package loads the ACE files from the (phred/phrap/consed) package by Phill Green. It was written to be used as a driver module for Bio::Assembly::IO input/output. =head2 Implemention Assemblies are loaded into Bio::Assembly::Scaffold objects composed by Bio::Assembly::Contig objects. In addition to default "_aligned_coord:$seqID" feature class from Bio::Assembly::Contig, contig objects loaded by this module will have the following special feature classes in their feature collection: "_align_clipping:$seqID" : location of subsequence in sequence $seqID which is aligned to the contig "_quality_clipping:$seqID" : location of good quality subsequence for sequence $seqID "consensus tags", as they are called in Consed's documentation, is equivalent to a bioperl sequence feature and, therefore, are added to the feature collection using their type field (see Consed's README.txt file) as primary tag. "read tags" are also sequence features and are stored as sub_SeqFeatures of the sequence's coordinate feature (the corresponding "_aligned_coord:$seqID" feature, easily accessed through get_seq_coord() method). "whole assembly tags" have no start and end, as they are not associated to any particular sequence in the assembly, and are added to the assembly's annotation collection using phrap as tag. =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 the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - 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 - Robson Francisco de Souza Email rfsouza@citri.iq.usp.br =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Assembly::IO::ace; use strict; use vars qw(@ISA); use Bio::Assembly::IO; use Bio::Assembly::Scaffold; use Bio::Assembly::Contig; use Bio::LocatableSeq; use Bio::Annotation::SimpleValue; use Bio::Seq::PrimaryQual; use Bio::SeqFeature::Generic; @ISA = qw(Bio::Assembly::IO); =head1 Parser methods =head2 next_assembly Title : next_assembly Usage : $unigene = $stream->next_assembly() Function: returns the next assembly in the stream Returns : Bio::Assembly::Scaffold object Args : NONE =cut sub next_assembly { my $self = shift; # Object reference local $/="\n"; # Resetting assembly data structure my $assembly = Bio::Assembly::Scaffold->new(-source=>'phrap'); # Looping over all ACE file lines my ($contigOBJ,$read_name); my $read_data = {}; # Temporary holder for read data while ($_ = $self->_readline) { # By now, ACE files hold a single assembly chomp; # Loading assembly information (ASsembly field) # (/^AS (\d+) (\d+)/) && do { # $assembly->_set_nof_contigs($1); # $assembly->_set_nof_sequences_in_contigs($2); # }; # Loading contig sequence (COntig sequence field) (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found! my $contigID = $1; $contigOBJ = Bio::Assembly::Contig->new(-source=>'phrap', -id=>$contigID); # $contigOBJ->set_nof_bases($2); # Contig length in base pairs # $contigOBJ->set_nof_reads($3); # Number of reads in this contig # $contigOBJ->set_nof_segments($4); # Number of read segments selected for consensus assembly my $ori = ($5 eq 'U' ? 1 : -1); # 'C' if contig was complemented (using consed) or U if not (default) $contigOBJ->strand($ori); my $consensus_sequence = undef; while ($_ = $self->_readline) { # Looping over contig lines chomp; # Drop <ENTER> (\n) on current line last if (/^$/); # Stop if empty line (contig end) is found s/\*/-/g; # Forcing '-' as gap symbol $consensus_sequence .= $_; } my $consensus_length = length($consensus_sequence); $consensus_sequence = Bio::LocatableSeq->new(-seq=>$consensus_sequence, -start=>1, -end=>$consensus_length, -id=>$contigID); $contigOBJ->set_consensus_sequence($consensus_sequence); $assembly->add_contig($contigOBJ); }; # Loading contig qualities... (Base Quality field) /^BQ/ && do { my $consensus = $contigOBJ->get_consensus_sequence()->seq(); my ($i,$j,@tmp); my @quality = (); $j = 0; while ($_ = $self->_readline) { chomp; last if (/^$/); @tmp = grep { /^\d+$/ } split(/\s+/); $i = 0; my $previous = 0; my $next = 0; while ($i<=$#tmp) { # IF base is a gap, quality is the average for neighbouring sites if (substr($consensus,$j,1) eq '-') { $previous = $tmp[$i-1] unless ($i == 0); if ($i < $#tmp) { $next = $tmp[$i+1]; } else { $next = 0; } push(@quality,int(($previous+$next)/2)); } else { push(@quality,$tmp[$i]); $i++; } $j++; } } my $qual = Bio::Seq::PrimaryQual->new(-qual=>join(" ",@quality), -id=>$contigOBJ->id()); $contigOBJ->set_consensus_quality($qual); }; # Loading read info... (Assembled From field) /^AF (\S+) (C|U) (-*\d+)/ && do { $read_name = $1; my $ori = $2; $read_data->{$read_name}{'padded_start'} = $3; # aligned start $ori = ( $ori eq 'U' ? 1 : -1); $read_data->{$read_name}{'strand'} = $ori; }; # Loading base segments definitions (Base Segment field) # /^BS (\d+) (\d+) (\S+)/ && do { # if (exists($self->{'contigs'}[$contig]{'reads'}{$3}{'segments'})) { # $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 . " " . $2; # } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} = $1 . " " . $2 } # }; # Loading reads... (ReaD sequence field /^RD (\S+) (-*\d+) (\d+) (\d+)/ && do { $read_name = $1; $read_data->{$read_name}{'length'} = $2; # number_of_padded_bases $read_data->{$read_name}{'contig'} = $contigOBJ; # $read_data->{$read_name}{'number_of_read_info_items'} = $3; # $read_data->{$read_name}{'number_of_tags'} = $4; my $read_sequence; while ($_ = $self->_readline) { chomp; last if (/^$/); s/\*/-/g; # Forcing '-' as gap symbol $read_sequence .= $_; # aligned read sequence } my $read = Bio::LocatableSeq->new(-seq=>$read_sequence, -start=>1, -end=>$read_data->{$read_name}{'length'}, -strand=>$read_data->{$read_name}{'strand'}, -id=>$read_name, -primary_id=>$read_name, -alphabet=>'dna'); # Adding read location and sequence to contig ("gapped consensus" coordinates) my $padded_start = $read_data->{$read_name}{'padded_start'}; my $padded_end = $padded_start + $read_data->{$read_name}{'length'} - 1; my $coord = Bio::SeqFeature::Generic->new(-start=>$padded_start, -end=>$padded_end, -strand=>$read_data->{$read_name}{'strand'}, -tag => { 'contig' => $contigOBJ->id } ); $contigOBJ->set_seq_coord($coord,$read); }; # Loading read trimming and alignment ranges... /^QA (-?\d+) (-?\d+) (-?\d+) (-?\d+)/ && do { my $qual_start = $1; my $qual_end = $2; my $align_start = $3; my $align_end = $4; unless ($align_start == -1 && $align_end == -1) { $align_start = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$align_start); $align_end = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$align_end); my $align_feat = Bio::SeqFeature::Generic->new(-start=>$align_start, -end=>$align_end, -strand=>$read_data->{$read_name}{'strand'}, -primary=>"_align_clipping:$read_name"); $align_feat->attach_seq( $contigOBJ->get_seq_by_name($read_name) ); $contigOBJ->add_features([ $align_feat ], 0); } unless ($qual_start == -1 && $qual_end == -1) { $qual_start = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$qual_start); $qual_end = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$qual_end); my $qual_feat = Bio::SeqFeature::Generic->new(-start=>$qual_start, -end=>$qual_end, -strand=>$read_data->{$read_name}{'strand'}, -primary=>"_quality_clipping:$read_name"); $qual_feat->attach_seq( $contigOBJ->get_seq_by_name($read_name) ); $contigOBJ->add_features([ $qual_feat ], 0); } }; # Loading read description (DeScription fields) # /^DS / && do { # /CHEM: (\S+)/ && do { # $self->{'contigs'}[$contig]{'reads'}{$read_name}{'chemistry'} = $1; # }; # /CHROMAT_FILE: (\S+)/ && do { # $self->{'contigs'}[$contig]{'reads'}{$read_name}{'chromat_file'} = $1; # }; # /DIRECTION: (\w+)/ && do { # my $ori = $1; # if ($ori eq 'rev') { $ori = 'C' } # elsif ($ori eq 'fwd') { $ori = 'U' } # $self->{'contigs'}[$contig]{'reads'}{$read_name}{'strand'} = $ori; # }; # /DYE: (\S+)/ && do { # $self->{'contigs'}[$contig]{'reads'}{$read_name}{'dye'} = $1; # }; # /PHD_FILE: (\S+)/ && do { # $self->{'contigs'}[$contig]{'reads'}{$read_name}{'phd_file'} = $1; # }; # /TEMPLATE: (\S+)/ && do { # $self->{'contigs'}[$contig]{'reads'}{$read_name}{'template'} = $1; # }; # /TIME: (\S+ \S+ \d+ \d+\:\d+\:\d+ \d+)/ && do { # $self->{'contigs'}[$contig]{'reads'}{$read_name}{'phd_time'} = $1; # }; # }; # Loading contig tags ('tags' in phrap terminology, but Bioperl calls them features) /^CT\s*\{/ && do { my ($contigID,$type,$source,$start,$end,$date) = split(' ',$self->_readline); $contigID =~ s/^Contig//i; my $extra_info = undef; while ($_ = $self->_readline) { last if (/\}/); $extra_info .= $_; } my $contig_tag = Bio::SeqFeature::Generic->new(-start=>$start, -end=>$end, -primary=>$type, -tag=>{ 'source' => $source, 'creation_date' => $date, 'extra_info' => $extra_info }); $assembly->get_contig_by_id($contigID)->add_features([ $contig_tag ],1); }; # Loading read tags /^RT\s*\{/ && do { my ($readID,$type,$source,$start,$end,$date) = split(' ',$self->_readline); my $extra_info = undef; while ($_ = $self->_readline) { last if (/\}/); $extra_info .= $_; } $start = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$start); $end = $contigOBJ->change_coord("aligned $read_name",'gapped consensus',$end); my $read_tag = Bio::SeqFeature::Generic->new(-start=>$start, -end=>$end, -primary=>$type, -tag=>{ 'source' => $source, 'creation_date' => $date, 'extra_info' => $extra_info }); my $contig = $read_data->{$readID}{'contig'}; my $coord = $contig->get_seq_coord( $contig->get_seq_by_name($readID) ); $coord->add_sub_SeqFeature($read_tag); }; # Loading read tags /^WA\s*\{/ && do { my ($type,$source,$date) = split(' ',$self->_readline); my $extra_info = undef; while ($_ = $self->_readline) { last if (/\}/); $extra_info = $_; } #? push(@line,\@extra_info); my $assembly_tag = join(" ","TYPE: ",$type,"PROGRAM:",$source, "DATE:",$date,"DATA:",$extra_info); $assembly_tag = Bio::Annotation::SimpleValue->new(-value=>$assembly_tag); $assembly->annotation->add_Annotation('phrap',$assembly_tag); }; } # while ($_ = $self->_readline) $assembly->update_seq_list(); return $assembly; } =head2 write_assembly Title : write_assembly Usage : $ass_io->write_assembly($assembly) Function: Write the assembly object in Phrap compatible ACE format Returns : 1 on success, 0 for error Args : A Bio::Assembly::Scaffold object =cut sub write_assemebly { my $self = shift; $self->throw("Writing phrap ACE files is not implemented yet! Sorry..."); } 1; __END__