Bio::Tools Coil
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Summary
Bio::Tools::Coil - parser for Coil output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
 use Bio::Tools::Coil
my $parser = Bio::Tools::Coil->new();
while( my $sp_feat = $parser->next_result($file) ) {
#do something
#eg
push @sp_feat, $sp_feat;
}
Description
 Parser for Coil output
Methods
new
No description
Code
parse_resultsDescriptionCode
next_resultDescriptionCode
_resultDescriptionCode
_add_predictionDescriptionCode
_predictions_parsedDescriptionCode
create_featureDescriptionCode
_read_fastaDescriptionCode
Methods description
parse_resultscode    nextTop
 Title   : parse_results
Usage : obj->parse_results
Function: Parses the coil output. Automatically called by
next_result() if not yet done.
Example :
Returns :
next_resultcodeprevnextTop
 Title   : next_result
Usage : while($feat = $coil->next_result($file)) {
# do something
}
Function: Returns the next protein feature of the coil output file
Returns :
Args :
_resultcodeprevnextTop
 Title   : _result
Usage : $feat = $obj->_result()
Function: internal
Example :
Returns :
_add_predictioncodeprevnextTop
 Title   : _add_prediction()
Usage : $obj->_add_prediction($feat)
Function: internal
Example :
Returns :
_predictions_parsedcodeprevnextTop
 Title   : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
create_featurecodeprevnextTop
 Title   : create_feature
Usage : obj->create_feature(\%feature)
Function: Internal(not to be used directly)
Returns :
Args :
_read_fastacodeprevnextTop
 Title   : _read_fasta
Usage : obj->_read_fasta($file)
Function: Internal(not to be used directly)
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
    $self->_initialize_io(@args);

    return $self;
}
parse_resultsdescriptionprevnextTop
sub parse_results {
    my ($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; } } } $self->_predictions_parsed(1);
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self,$resfile) = @_;
    my $gene;

    $self->parse_results($resfile) unless $self->_predictions_parsed();

    $gene = $self->_result();

    return $gene;
}
_resultdescriptionprevnextTop
sub _result {
    my ($self) = @_;

    return unless(exists($self->{'_feats'}) && @{$self->{'_feats'}});
    return shift(@{$self->{'_feats'}});
}
_add_predictiondescriptionprevnextTop
sub _add_prediction {
    my ($self, $gene) = @_;

    if(! exists($self->{'_feats'})) {
        $self->{'_feats'} = [];
    }
    push(@{$self->{'_feats'}}, $gene);
}
_predictions_parseddescriptionprevnextTop
sub _predictions_parsed {
    my ($self, $val) = @_;

    $self->{'_preds_parsed'} = $val if $val;
    if(! exists($self->{'_preds_parsed'})) {
        $self->{'_preds_parsed'} = 0;
    }
    return $self->{'_preds_parsed'};
}
create_featuredescriptionprevnextTop
sub create_feature {
    my ($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;
}
_read_fastadescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
 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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
Reporting BugsTop
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
 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>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
APPENDIXTop
 The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _