Raw content of Bio::SeqIO::FTHelper # $Id: FTHelper.pm,v 1.55 2002/11/05 02:55:12 lapp Exp $ # # BioPerl module for Bio::SeqIO::FTHelper # # Cared for by Ewan Birney <birney@ebi.ac.uk> # # Copyright Ewan Birney # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables =head1 SYNOPSIS Used by Bio::SeqIO::EMBL to help process the Feature Table =head1 DESCRIPTION Represents one particular Feature with the following fields key - the key of the feature loc - the location string of the feature <other fields> - other fields =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 - Ewan Birney Email birney@ebi.ac.uk Describe contact details here =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::FTHelper; use vars qw(@ISA); use strict; use Bio::SeqFeature::Generic; use Bio::Location::Simple; use Bio::Location::Fuzzy; use Bio::Location::Split; use Bio::Root::Root; @ISA = qw(Bio::Root::Root); sub new { my ($class, @args) = @_; # no chained new because we make lots and lots of these. my $self = {}; bless $self,$class; $self->{'_field'} = {}; return $self; } =head2 _generic_seqfeature Title : _generic_seqfeature Usage : $fthelper->_generic_seqfeature($annseq, "GenBank") Function: processes fthelper into a generic seqfeature Returns : TRUE on success and otherwise FALSE Args : The Bio::Factory::LocationFactoryI object to use for parsing location strings. The ID (e.g., display_id) of the sequence on which this feature is located, optionally a string indicating the source (GenBank/EMBL/SwissProt) =cut sub _generic_seqfeature { my ($fth, $locfac, $seqid, $source) = @_; my ($sf); # set a default if not specified if(! defined($source)) { $source = "EMBL/GenBank/SwissProt"; } # initialize feature object $sf = Bio::SeqFeature::Generic->direct_new(); # parse location; this may cause an exception, in which case we gently # recover and ignore this feature my $loc; eval { $loc = $locfac->from_string($fth->loc); }; if(! $loc) { $fth->warn("exception while parsing location line [" . $fth->loc . "] in reading $source, ignoring feature " . $fth->key() . " (seqid=" . $seqid . "): " . $@); return; } # set additional location attributes if($seqid && (! $loc->is_remote())) { $loc->seq_id($seqid); # propagates if it is a split location } # set attributes of feature $sf->location($loc); $sf->primary_tag($fth->key); $sf->source_tag($source); foreach my $key ( keys %{$fth->field} ){ foreach my $value ( @{$fth->field->{$key}} ) { $sf->add_tag_value($key,$value); } } return $sf; } =head2 from_SeqFeature Title : from_SeqFeature Usage : @fthelperlist = Bio::SeqIO::FTHelper::from_SeqFeature($sf, $context_annseq); Function: constructor of fthelpers from SeqFeatures : : The additional annseq argument is to allow the building of FTHelper : lines relevant to particular sequences (ie, when features are spread over : enteries, knowing how to build this) Returns : an array of FThelpers Args : seq features =cut sub from_SeqFeature { my ($sf, $context_annseq) = @_; my @ret; # # If this object knows how to make FThelpers, then let it # - this allows us to store *really* weird objects that can write # themselves to the EMBL/GenBank... # if ( $sf->can("to_FTHelper") ) { return $sf->to_FTHelper($context_annseq); } my $fth = Bio::SeqIO::FTHelper->new(); my $key = $sf->primary_tag(); my $locstr = $sf->location->to_FTstring; # ES 25/06/01 Commented out this code, Jason to double check #The location FT string for all simple subseqfeatures is already #in the Split location FT string # going into sub features #foreach my $sub ( $sf->sub_SeqFeature() ) { #my @subfth = &Bio::SeqIO::FTHelper::from_SeqFeature($sub); #push(@ret, @subfth); #} $fth->loc($locstr); $fth->key($key); $fth->field->{'note'} = []; #$sf->source_tag && do { push(@{$fth->field->{'note'}},"source=" . $sf->source_tag ); }; ($sf->can('score') && $sf->score) && do { push(@{$fth->field->{'note'}}, "score=" . $sf->score ); }; ($sf->can('frame') && $sf->frame) && do { push(@{$fth->field->{'note'}}, "frame=" . $sf->frame ); }; #$sf->strand && do { push(@{$fth->field->{'note'}},"strand=" . $sf->strand ); }; foreach my $tag ( $sf->all_tags ) { # Tags which begin with underscores are considered # private, and are therefore not printed next if $tag =~ /^_/; if ( !defined $fth->field->{$tag} ) { $fth->field->{$tag} = []; } foreach my $val ( $sf->each_tag_value($tag) ) { push(@{$fth->field->{$tag}},$val); } } push(@ret, $fth); unless (@ret) { $context_annseq->throw("Problem in processing seqfeature $sf - no fthelpers. Error!"); } foreach my $ft (@ret) { if ( !$ft->isa('Bio::SeqIO::FTHelper') ) { $sf->throw("Problem in processing seqfeature $sf - made a $fth!"); } } return @ret; } =head2 key Title : key Usage : $obj->key($newval) Function: Example : Returns : value of key Args : newvalue (optional) =cut sub key { my ($obj, $value) = @_; if ( defined $value ) { $obj->{'key'} = $value; } return $obj->{'key'}; } =head2 loc Title : loc Usage : $obj->loc($newval) Function: Example : Returns : value of loc Args : newvalue (optional) =cut sub loc { my ($obj, $value) = @_; if ( defined $value ) { $obj->{'loc'} = $value; } return $obj->{'loc'}; } =head2 field Title : field Usage : Function: Example : Returns : Args : =cut sub field { my ($self) = @_; return $self->{'_field'}; } =head2 add_field Title : add_field Usage : Function: Example : Returns : Args : =cut sub add_field { my ($self, $key, $val) = @_; if ( !exists $self->field->{$key} ) { $self->field->{$key} = []; } push( @{$self->field->{$key}} , $val); } 1;