Bio::Tools::Run Prints
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Tools::Run::Prints
Package variables
No package variables defined.
Included modules
Bio::Factory::ApplicationFactoryI
Bio::Root::IO
Bio::Root::Root
Bio::SeqIO
Bio::Tools::Prints
Bio::Tools::Run::WrapperBase
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  Build a Prints factory

  my @params = ('DB',$dbfile);
  my $factory = Bio::Tools::Run::Prints->new($params);

  # Pass the factory a Bio::Seq object
  # @feats is an array of Bio::SeqFeature::Generic objects
  my @feats = $factory->run($seq);
Description
  FingerPRINTScan II is a PRINTS fingerprint identification algorithm.
  Copyright (C) 1998,1999  Phil Scordis
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
AUTOLOAD
No description
Code
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   : $prints->new(@params)
 Function: creates a new Prints factory
 Returns:  Bio::Tools::Run::Prints
 Args    :
predict_protein_featurescodeprevnextTop
 Title   :   predict_protein_features()
 Usage   :   DEPRECATED. Use $obj->run($seqFile) instead.
 Function:   Runs Prints 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 Prints 
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI, or a Fasta file name
_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 {
       @PRINTS_PARAMS=qw(DB PROGRAM VERBOSE);
       foreach my $attr ( @PRINTS_PARAMS)
                        { $OK_FIELD{$attr}++;
}
program_namedescriptionprevnextTop
sub program_name {
  return 'FingerPRINTScan';
}
program_dirdescriptionprevnextTop
sub program_dir {
return Bio::Root::IO->catfile($ENV{PRINTSDIR}) if $ENV{PRINTSDIR};
}
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};
}
newdescriptionprevnextTop
sub new {
       my ($class,@args) = @_;
       my $self = $class->SUPER::new(@args);
       $self->io->_initialize_io();
 
       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 clone object is not a seq object but a 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 ($tfh,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
     close($tfh);
     undef $tfh;
     my $str =$self->executable." ".$self->DB." ".$self->_input." -fjR >".$outfile;
     my $status = system($str);
     $self->throw( "Prints call ($str) crashed: $?\n ") unless $status==0;
     
     my $filehandle;
     if (ref ($outfile) !~ /GLOB/) {
        open (PRINTS, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
        $filehandle =\* PRINTS;
     }
     else {
        $filehandle = $outfile;
     }
     my $prints_parser = Bio::Tools::Prints->new(-fh=>$filehandle);
     my @prints_feat;
     
     while(my $prints_feat = $prints_parser->next_result){
         push @prints_feat, $prints_feat;
     }
     
     
     $self->cleanup();
     unlink $outfile;    
     return @prints_feat;
}
_writeSeqFiledescriptionprevnextTop
sub _writeSeqFile {
    my ($self,$seq) = @_;
    my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir());
    my $in  = Bio::SeqIO->new(-fh => $tfh , '-format' => 'Fasta');
    $in->write_seq($seq);
    $in->close();
    undef $in;
    close($tfh);
    undef $tfh;
    return $inputfile;

}
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 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://redmine.open-bio.org/projects/bioperl/
AUTHOR - BalaTop
 Email savikalpa@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    :