Raw content of Bio::Assembly::IO::phrap # $Id: phrap.pm,v 1.1 2002/11/04 14:38:14 heikki Exp $ # # BioPerl driver for phrap.out file # # 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::phrap - driver to load phrap.out files. =head1 SYNOPSYS # Building an input stream use Bio::Assembly::IO; # Assembly loading methods $io = new Bio::Assembly::IO(-file=>"SGC0-424.phrap.out", -format=>"phrap"); $assembly = $io->next_assembly; =head1 DESCRIPTION This package was developed to load the phrap.out files from the (phred/phrap/consed) package by Phill Green. This files contain just the messages printed to standard out by phrap when building an assembly. This output is redirected by phredPhrap perl-script to a file in the project's directory and hold some bit of information regarding assembly quality, connections between contigs and clone's position inside contigs. It should be noted that such files have no data about the sequence. neither for contig consensus nor for any aligned sequence. Anyway, such information may be loaded from Fasta files in the projects directory and added to the assembly object later. Note that, because no sequence is loaded for the contig consensus and locations for aligned sequences are only given in "ungapped consensus" coordinates in a phrap.out file, you can't make coordinate changes in assemblies loaded by pharp.pm, unless you add an aligned coordinates for each sequence to each contig's features collection yourself. See L<Bio::Assembly::Contig::Coordinate_Systems> and L<Bio::Assembly::Contig::Feature_collection>.. This driver also loads singlets into the assembly contigs as Bio::Seq objects, altough without their sequence strings. It also adds a feature for the entire sequence, thus storing the singlet length in its end position, and adds a tag '_nof_trimmed_nonX' to the feature, which stores the number of non-vector bases in the singlet. =head2 Implementation Assemblies are loaded into Bio::Assembly::Scaffold objects composed by Bio::Assembly::Contig objects. No features are added to Bio::Assembly::Contig "_aligned_coord:$seqID" feature class, therefore you can't make coordinate changes in contigs loaded by this module. Contig objects created by this module will have the following special feature classes, identified by their primary tags, in their features collection: "_main_contig_feature:$ID" : main feature for contig $ID. This feature is used to store information about the entire consensus sequence. This feature always start at base 1 and its end position is the consensus sequence length. A tag, 'trimmed_length' holds the length of the trimmed good quality region inside the consensus sequence. "_covered_region:$index" : coordinates for valid clones inside the contig. $index is the covered region number, starting at 1 for the covered region closest to the consensus sequence first base. "_unalign_coord:$seqID" : location of a sequence in "ungapped consensus" coordinates (consensus sequence without gaps). Primary and secondary scores, indel and substitutions statistics are stored as feature tags. "_internal_clones:$cloneID" : clones inside contigs $cloneID should be used as the unique id for each clone. These features have six tags: '_1st_name', which is the id of the upstream (5') aligned sequence delimiting the clone; '_1st_strand', the upstream sequence strand in the alignment; '_2nd_name', downstream (3') sequence id; '_2nd_strand', the downstream sequence strand in the alignment; '_length', unaligned clone length; '_rejected', a boolean flag, which is false if the clone is valid and true if it was rejected. All coordinates for the features above are expressed as "ungapped consensus" coordinates (See L<Bio::Assembly::Contig::Coordinate_Systems>.. =head2 Feature collection # =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::phrap; use strict; use vars qw(@ISA); use Bio::Assembly::IO; use Bio::Assembly::Scaffold; use Bio::Assembly::Contig; use Bio::LocatableSeq; use Bio::Seq; use Bio::SeqFeature::Generic; @ISA = qw(Bio::Assembly::IO); =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; # Package reference # Resetting assembly data structure my $Assembly = Bio::Assembly::Scaffold->new(-source=>'phrap'); # Looping over all phrap out file lines my ($contigOBJ); while ($_ = $self->_readline) { chomp; # Loading exact dupicated reads list # /Exact duplicate reads:/ && do { # my @exact_dupl; # while (<FILE>) { # last if (/^\s*$/); # /(\S+)\s+(\S+)/ && do { # push(@exact_dupl,[$1,$2]); # }; # $self->{'assembly'}{'exact_dupl_reads'} = # new Data::Table(\@exact_dupl,['included','excluded'],0); # } # }; # Loading singlets reads data /^(\d+) isolated singletons/ && do { while ($_ = $self->_readline) { chomp; last if (/^$/); if (/^\s+(\S+)\s+(\d+)\s+\((\d+)\)/) { my $seqID = $1; my $length = $2; my $nof_trimmed_nonX = $3; my $seq = new Bio::Seq(-strand=>1, -primary_id=>$seqID); my $f = Bio::SeqFeature::Generic->new (-start=>1, -end=>$seq->length(), -primary=>$seq->primary_id(), -tag=>{ '_nof_trimmed_nonX' => $nof_trimmed_nonX } ); $seq->add_SeqFeature($f); $Assembly->add_singlet($seq); } } }; # Loading contig information /^Contig (\d+)\.\s+(\d+) reads?; (\d+) bp \(untrimmed\), (\d+) \(trimmed\)\./ && do { my $nof_reads = $2; my $length = $3; my $trimmed_length = $4; $contigOBJ = Bio::Assembly::Contig->new(-id=>$1, -source=>'phrap'); my $feat = Bio::SeqFeature::Generic->new(-start=>1, -end=>$length, -primary=>"_main_contig_feature:".$contigOBJ->id(), -tag=>{ '_trimmed_length' => $trimmed_length } ); $contigOBJ->add_features([ $feat ],1); $Assembly->add_contig($contigOBJ); }; # Loading read information /^(C?)\s+(-?\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+\(\s*(\d+)\)\s+(\d+\.\d*)\s+(\d+\.\d*)\s+(\d+\.\d*)/ && do { my $strand = ($1 eq 'C' ? -1 : 1); my $readID = $4; my $start = $2; my $end = $3; my $primary_score = $5; my $secondary_score = $6; my $substitutions = $7; my $deletions = $8; my $insertions = $9; my $seq = Bio::LocatableSeq->new(-start=>$start, -end=>$end, -strand=>$strand, -id=>$readID, -primary_id=>$readID, -alphabet=>'dna'); my $unalign_coord = Bio::SeqFeature::Generic->new(-start=>$start, -end=>$end, -primary=>"_unalign_coord:$readID", -tag=>{'_primary_score'=>$primary_score, '_secondary_score'=>$secondary_score, '_substitutions'=>$substitutions, '_insertions'=>,$insertions, '_deletions'=>$deletions } ); $unalign_coord->attach_seq($seq); $contigOBJ->add_seq($seq); $contigOBJ->add_features([ $unalign_coord ]); }; # Loading INTERNAL clones description /INTERNAL\s+Contig\s+(\d+)\s+opp\s+sense/ && do { my $contigID = $1; my $contig = $Assembly->get_contig_by_id($contigID); while ($_ = $self->_readline) { my (@data,$rejected,$c1_strand,$c2_strand); (@data = /\s+(\*?)\s+(C?)\s+(\S+)\s+(C?)\s+(\S+)\s+(-?\d+)\s+(-?\d+)\s+(-?\d+)/) && do { if ($data[0] eq '*') { $rejected = 1 } else { $rejected = 0 } $c1_strand = ($data[1] eq 'C' ? -1 : 1); $c2_strand = ($data[3] eq 'C' ? -1 : 1); (my $clone_name = $data[2]) =~ s/^(\S+)\.\w.*/$1/; my $clone = Bio::SeqFeature::Generic->new(-start=>$data[6], -end=>$data[7], -strand=>0, -primary=>"_internal_clone:$clone_name", -tag=>{'_1st_strand'=>,$c1_strand, '_2nd_strand'=>,$c2_strand, '_1st_name'=>$data[2], '_2nd_name'=>$data[4], '_length'=>$data[5], '_rejected'=>$rejected } ); $contig->add_features([ $clone ]); }; /Covered regions:/ && do { my %coord = /(\d+)/g; my $i = 0; foreach my $start (sort { $a <=> $b } keys %coord) { my $cov = Bio::SeqFeature::Generic->new(-start=>$start, -end=>$coord{$start}, -primary=>'_covered_region:'.++$i ); # 1: attach feature to contig consensus, if any $contig->add_features([ $cov ],1); } last; # exit while loop }; # /Covered regions:/ } # while ($_ = $self->_readline) }; # /INTERNAL\s+Contig\s+(\d+)\s+opp\s+sense/ } # while ($_ = $self->_readline) 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.out files is not implemented yet! Sorry..."); } 1; __END__