Bio::Tools::Run Coil
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Summary
Bio::Tools::Run::Coil - wrapper for ncoils program
Package variables
No package variables defined.
Included modules
Bio::Root::IO
Bio::Root::Root
Bio::SeqIO
Bio::Tools::Coil
Bio::Tools::Run::WrapperBase
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  # Build a Coil factory
my $factory = Bio::Tools::Run::Coil->new($params);
# Pass the factory a Bio::Seq object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq);
Description
This module is a wrapper for the ncoils program available via
http://www.russell.embl-heidelberg.de/coils/coils.tar.gz for predicting
coiled coils in protein sequences.
By default it looks for an executable called ncoils and data/parameter files
in the directory specified by the COILSDIR environmental variable.
Methods
BEGIN Code
AUTOLOAD
No description
Code
program_nameDescriptionCode
program_dirDescriptionCode
newDescriptionCode
predict_protein_featuresDescriptionCode
runDescriptionCode
_input()
No description
Code
_runDescriptionCode
_writeSeqFileDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
newcodeprevnextTop
 Title   : new
Usage : $coil->new(@params)
Function: creates a new Coil factory
Returns: Bio::Tools::Run::Coil
Args :
predict_protein_featurescodeprevnextTop
 Title   :   predict_protein_features()
Usage : DEPRECATED. Use $obj->run instead.
Function: Runs Coil and creates an array of featrues
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
run codeprevnextTop
 Title   :   run
Usage : $obj->run($seq)
Function: Runs Coil and creates an array of featrues
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI, or a Fasta filename.
_runcodeprevnextTop
 Title   :   _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : An array of Bio::SeqFeature::Generic objects
Args :
_writeSeqFilecodeprevnextTop
 Title   :   _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns :
Args :
Methods code
BEGINTop
BEGIN {
       @COIL_PARAMS=qw(PROGRAM VERBOSE QUIET SILENT);
       foreach my $attr ( @COIL_PARAMS)
                        { $OK_FIELD{$attr}++;
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
       my $self = shift;
       my $attr = $AUTOLOAD;
       $attr =~ s/.*:://;
       $attr = uc $attr;
       $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
       $self->{$attr} = shift if @_;
       return $self->{$attr};
}
program_namedescriptionprevnextTop
sub program_name {
    return 'ncoils';
}
program_dirdescriptionprevnextTop
sub program_dir {
    return Bio::Root::IO->catfile($ENV{COILSDIR}) if $ENV{COILSDIR};
}
newdescriptionprevnextTop
sub new {
       my ($class,@args) = @_;
       my $self = $class->SUPER::new(@args); 
       my ($attr, $value);
       while (@args)  {
           $attr =   shift @args;
           $value =  shift @args;
           next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/PROGRAM/i) { $self->executable($value); next; } $self->$attr($value); } return $self;
}
predict_protein_featuresdescriptionprevnextTop
sub predict_protein_features {
	return shift->run(@_);
}
rundescriptionprevnextTop
sub run {
    my ($self,$seq) = @_;
    my @feats;
    
    if (ref($seq) ) { # it is an object
if (ref($seq) =~ /GLOB/) { $self->throw("cannot use filehandle"); } my $infile1 = $self->_writeSeqFile($seq); $self->_input($infile1); @feats = $self->_run(); unlink $infile1; } else { #The argument is not a seq object but a sequence in a fasta file.
#Perhaps should check here or before if this file is fasta format...if not die
#Here the file does not need to be created or deleted. Its already written and may be used by other runnables.
$self->_input($seq); @feats = $self->_run(); } return @feats;
}
_input()descriptionprevnextTop
sub _input() {
    my ($self,$infile1) = @_;
    if(defined $infile1){
	
	$self->{'input'}=$infile1;
     }
    return $self->{'input'};
}
_rundescriptionprevnextTop
sub _run {
     my ($self)= @_;
     
     my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
     my $str =$self->executable." -f < ".$self->{'input'}." > ".$outfile;
     if($self->quiet || $self->verbose <=0 || $self->silent){
         $str.=" 2>/dev/null";
     }
     my $status = system($str);
     $self->throw( "Coil call ($str) crashed: $?\n ") unless $status==0;
     
     my $coil_parser = Bio::Tools::Coil->new();
     my $filehandle;
     if (ref ($outfile) !~ /GLOB/) {
        open (COIL, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
        $filehandle =\* COIL;
     }
     else {
        $filehandle = $outfile;
     }

     my @coil_feat; 
      
     while(my $coil_feat = $coil_parser->next_result($filehandle)){

          push @coil_feat, $coil_feat;
     }
     
     $self->cleanup();
     close($tfh1);
     undef $tfh1;

     unlink $outfile;
     return @coil_feat;
}
_writeSeqFiledescriptionprevnextTop
sub _writeSeqFile {
    my ($self,$seq) = @_;
    my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir());
    my $in  = Bio::SeqIO->new(-fh => $tfh , '-format' => 'Fasta');
    $in->write_seq($seq);

    return $inputfile;

}
1;
}
General documentation
REFERENCESTop
Lupas, van Dyke & Stock,
Predicting coiled coils from protein sequences,
Science 252:1162-1164, 1991.
Lupas, A.,
Prediction and Analysis of Coiled-Coil Structures,
Meth. Enzymology 266:513-525, 1996.
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 one
of the Bioperl mailing lists. 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
the bugs and their resolution. Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
AUTHORSTop
 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 _
_inputTop
 Title   :   _input
Usage : obj->_input($seqFile)
Function: Internal(not to be used directly)
Returns :
Args :