# $Id: arp.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::AlignIO::arp # # Copyright Chris Fields # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::AlignIO::arp - ARP MSA Sequence input/output stream =head1 SYNOPSIS Do not use this module directly. Use it via the L class. =head1 DESCRIPTION This object can create L objects from ARP flat files. These are typically configuration-like data files for the program Arlequin. For more information, see: http://lgb.unige.ch/arlequin/ For the moment, this retains the allele sequence data in the DATA section and inserts them into SimpleAlign objects. ARP files that contain other data (RFLP, etc.) are not expected to parse properly. Also, if the DNA data is actually SNP data, then the LocatableSeq object instantiation will throw an error. This is now set up as a generic parser (i.e. it parses everything) and collects as much data as possible into the SimpleAlign object. The following in a general mapping of where data can be found: Tag SimpleAlign Method ---------------------------------------------------------------------- Title description SampleName id ---------------------------------------------------------------------- Tag Bio::Annotation TagName Bio::Annotation Class Parameters ---------------------------------------------------------------------- NE SimpleValue pfam_family_accession value NL SimpleValue sequence_start_stop value SS SimpleValue sec_structure_source value BM SimpleValue build_model value RN Reference reference * ---------------------------------------------------------------------- * RN is generated based on the number of Bio::Annotation::Reference objects In addition, the number of samples found in the alignment is retained in a Bio::Annotation::TagTree object in the annotation collection and is accessible via: ($samples) = $aln->annotation->get_Annotations('Samples'); say $samples->display_text; # or use other relevant TagTree methods to retrieve data =head1 FEEDBACK =head2 Support Please direct usage questions or support issues to the mailing list: I rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. =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 the web: http://bugzilla.open-bio.org/ =head1 AUTHORS Chris Fields (cjfields) =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::AlignIO::arp; use strict; use base qw(Bio::AlignIO); use Data::Dumper; use Bio::Annotation::AnnotationFactory; =head2 next_aln Title : next_aln Usage : $aln = $stream->next_aln Function: returns the next alignment in the stream. Returns : Bio::Align::AlignI object - returns 0 on end of file or on error Args : -width => optional argument to specify the width sequence will be written (60 chars by default) See L =cut sub next_aln { my $self = shift; my $aln = Bio::SimpleAlign->new(-source => 'arp'); my ($data, $cur_block, $cur_type, $cur_data); SCAN: while (defined ($data = $self->_readline) ) { next if $data =~ m{^\s*$}xms; if ($data =~ m{\[{1,2}(\w+)\]{1,2}}xms) { $self->{state}->{current_block} = $1; next SCAN; } elsif ($data =~ m{^\s*(\w+)=\s?(\S[^\n]*$)}xms) { ($cur_type, $cur_data) = ($1, $2); if ($cur_data =~ m{^\s*\{\s*$}) { $self->throw("Curly block must be embedded in a named Block") if !exists($self->{state}->{current_block}); $self->{state}->{in_curly_block} = 1; next SCAN; } $cur_data =~ s{["']}{}g; $cur_data =~ s{\s*$}{}; # per alignment annotation data (i.e. Sample Blocks) or # annotation data retained for each alignment? $self->{state}->{current_block} eq 'Samples' ? push @{$self->{state}->{SampleAnnotation}->{$cur_type}}, $cur_data : push @{$self->{state}->{Annotation}->{$cur_type}}, $cur_data; } elsif ($data =~ m{^\s*\}\s*$}xms) { $self->throw("Unmatched bracket in ARP file:\n$data") if !exists($self->{state}->{in_curly_block}); if ($self->{state}->{current_block} eq 'Samples') {; my $ac = $self->_process_annotation($aln); delete $self->{state}->{SampleAnnotation}; } else { # process other data at a later point } delete $self->{state}->{blockdata}; $self->{state}->{in_curly_block} = 0; last SCAN; } else { # all other data should be in a curly block and have a block title $self->throw("Data found outside of proper block:\n$data") if !exists($self->{state}->{current_block}) && !$self->{state}->{in_curly_block}; # bypass commented stuff (but we may want to process it at a later # point, so turn back here) next if $data =~ m{^\s*\#}xms; if ($self->{state}->{current_block} eq 'Samples') { chomp $data; # we have two possible ways to deal with sample number, either # clone the LocatableSeq (in which case we need to deal with ID # duplication), or store as annotation data. I chose the latter # route using a Bio::Annotation::TagTree. YMMV - cjfields 10-15-08 my ($ls, $samples) = $self->_process_sequence($data); my $id = $ls->id; push @{ $self->{state}->{SampleAnnotation}->{Samples} }, [$id => $samples]; $aln->add_seq($ls); } else { # add elsif's for further processing #$self->debug('Unmatched data in block '. # $self->{state}->{current_block}. # ":\n$data\n"); $self->{state}->{blockdata} .= $data; } } } # alignments only returned if they contain sequences return $aln if $aln->num_sequences; return; } =head2 write_aln Title : write_aln Usage : $stream->write_aln(@aln) Function: writes the $aln object into the stream in xmfa format Returns : 1 for success and 0 for error Args : L object See L =cut sub write_aln { my ($self,@aln) = @_; $self->throw_not_implemented; } ################ PRIVATE SUBS ################ sub _process_sequence { my ($self, $raw) = @_; return unless defined $raw; $raw =~ s{(?:^\s+|\s+$)}{}g; my ($id, $samples, $seq) = split(' ', $raw); my $ls = Bio::LocatableSeq->new(-seq => $seq, -start => 1, -id => $id); return($ls, $samples); } sub _process_annotation { my ($self, $aln) = @_; my $coll = Bio::Annotation::Collection->new(); my $factory = Bio::Annotation::AnnotationFactory->new(-type => 'Bio::Annotation::SimpleValue'); for my $anntype (qw(SampleAnnotation Annotation)) { for my $key (keys %{ $self->{state}->{$anntype} }) { if ($key eq 'Title') { $aln->description($self->{state}->{$anntype}->{$key}[0]); } elsif ($key eq 'Samples') { $factory->type('Bio::Annotation::TagTree'); $coll->add_Annotation($key, $factory->create_object( -value => [$key => $self->{state}->{$anntype}->{$key}])); $factory->type('Bio::Annotation::SimpleValue'); } elsif ($key eq 'SampleName') { $aln->id($self->{state}->{$anntype}->{$key}[0]); } else { $self->throw('Expecting an array reference') unless ref $self->{state}->{$anntype}->{$key} eq 'ARRAY'; for my $a (@{ $self->{state}->{$anntype}->{$key} }) { $coll->add_Annotation($key, $factory->create_object( -value => $a) ); } } } } #$self->debug("Collection:".Dumper($coll)."\n"); $aln->annotation($coll); } 1;