Raw content of Bio::Tools::Coil # Parser module for Coil Bio::Tools::Coil # # Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil # originally written by Marc Sohrmann (ms2@sanger.ac.uk) # Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org> # Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org) # You may distribute this module under the same terms as perl itself # # POD documentation - main docs before the code =head1 NAME Bio::Tools::Coil =head1 SYNOPSIS use Bio::Tools::Coil my $parser = new Bio::Tools::Coil(); while( my $sp_feat = $parser->next_result($file) ) { #do something #eg push @sp_feat, $sp_feat; } =head1 DESCRIPTION Parser for Coil output =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil originally written by Marc Sohrmann (ms2@sanger.ac.uk) Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org> Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org) =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Tools::Coil; use vars qw(@ISA); use strict; use Bio::Root::Root; use Bio::SeqFeature::FeaturePair; use Bio::Root::IO; use Bio::SeqFeature::Generic; @ISA = qw(Bio::Root::Root Bio::Root::IO); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 parse_results Title : parse_results Usage : obj->parse_results Function: Parses the coil output. Automatically called by next_result() if not yet done. Example : Returns : =cut sub parse_results { my ($self,$resfile) = @_; my $filehandle = $resfile; my %result_hash =_read_fasta($filehandle);#bala no file handle my @ids = keys %result_hash; my @feats; foreach my $id (keys %result_hash){ my $pep = reverse ($result_hash{$id}); my $count = my $switch = 0; my ($start, $end); while (my $aa = chop $pep) { $count++; if (!$switch && $aa eq "x") { $start = $count; $switch = 1; } elsif ($switch && $aa ne "x") { $end = $count-1; my (%feature); $feature{name} = $id; $feature{start} = $start; $feature{end} = $end; $feature{source} = "Coils"; $feature{primary} = 'ncoils'; ($feature{program}) = 'ncoils'; $feature{logic_name} = 'Coils'; my $new_feat = $self->create_feature (\%feature); $self->_add_prediction($new_feat); $switch = 0; } } } $self->_predictions_parsed(1); } =head2 next_result Title : next_result Usage : while($feat = $coil->next_result($file)) { # do something } Function: Returns the next protein feature of the coil output file Returns : Args : =cut sub next_result{ my ($self,$resfile) = @_; my $gene; $self->parse_results($resfile) unless $self->_predictions_parsed(); $gene = $self->_result(); return $gene; } =head2 _result Title : _result Usage : $feat = $obj->_result() Function: internal Example : Returns : =cut sub _result{ my ($self) = @_; return undef unless(exists($self->{'_feats'}) && @{$self->{'_feats'}}); return shift(@{$self->{'_feats'}}); } =head2 _add_prediction Title : _add_prediction() Usage : $obj->_add_prediction($feat) Function: internal Example : Returns : =cut sub _add_prediction { my ($self, $gene) = @_; if(! exists($self->{'_feats'})) { $self->{'_feats'} = []; } push(@{$self->{'_feats'}}, $gene); } =head2 _predictions_parsed Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE =cut sub _predictions_parsed { my ($self, $val) = @_; $self->{'_preds_parsed'} = $val if $val; if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } =head2 create_feature Title : create_feature Usage : obj->create_feature(\%feature) Function: Internal(not to be used directly) Returns : Args : =cut sub create_feature { my ($self, $feat) = @_; # create feature object my $feature = Bio::SeqFeature::Generic->new(-seq_id => $feat->{name}, -start => $feat->{start}, -end => $feat->{end}, -score => $feat->{score}, -source => $feat->{source}, -primary => $feat->{primary}, -logic_name => $feat->{logic_name}, ); $feature->add_tag_value('evalue',0); $feature->add_tag_value('percent_id','NULL'); $feature->add_tag_value("hid",$feat->{primary}); return $feature; } =head2 _read_fasta Title : _read_fasta Usage : obj->_read_fasta($file) Function: Internal(not to be used directly) Returns : Args : =cut sub _read_fasta { local (*FILE) = @_; my( $id , $seq , %name2seq);#bala while (<FILE>) { chomp;#bala if (/^>(\S+)/) { my $new_id = $1; if ($id) { $name2seq{$id} = $seq; } $id = $new_id ; $seq = "" ; } elsif (eof) { if ($id) { $seq .= $_ ;#bala line instead of $_ $name2seq{$id} = $seq; } } else { $seq .= $_ } } return %name2seq; } 1;