Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation Prodom
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Summary
Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Prodom
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation
Synopsis
  # something like this
my $query = new Bio::Seq(-file => $queryfile,
-format => 'Fasta');
my $hmm = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Prodom->new ('-query' => $query, '-program' => 'hmmpfam' or '/usr/local/pubseq/bin/hmmpfam', '-database' => 'sf_hmm'); $hmm->workdir ($workdir); $hmm->run; my @results = $hmm->output;
Description
  Blast takes a Bio::Seq (or Bio::PrimarySeq) object and runs hmmpfam.
The resulting output file is parsed to produce a set of Bio::EnsEMBL::FeaturePairs.
Methods
parse_resultsDescriptionCode
run_analysis
No description
Code
Methods description
parse_resultscode    nextTop
 Title    :  parse_results
Usage : $self->parse_results ($filename)
Function : parses program output to give a set of features
Example :
Returns :
Args : filename (optional, can be filename, filehandle or pipe, not implemented)
Throws :
Methods code
parse_resultsdescriptionprevnextTop
sub parse_results {
  my ($self) = @_;

  my $filehandle;
  my $resfile = $self->resultsfile();
  my @fps;
 		


  if (-e $resfile) {
	if (-z $self->resultsfile) {  
	    print STDERR "Prodom didn't find any hits\n";
	    return; }       
	else {
	    open (CPGOUT, "<$resfile") or $self->throw("Error opening ", $resfile, "\n ");#
} } #5_Translation_id_5_gene_5 1 40 // pd_PD000035;sp_TLL_DROVI_O16845; 33 102 // S=135 E=2e-08 // (1021) RECEPTOR NUCLEAR TRANSCRIPTION DNA-BINDING REGULATION ZINC-FINGER METAL-BINDING ZINC HORMONE FAMILY Length = 70
# Example output:
#CE27771 203 318 // pd_PD002460;sp_Q19242_CAEEL_Q19242; 199 344 // S=122 E=6e-06 // (189) BIOSYNTHESIS MOLYBDOPTERIN MOEA COFACTOR MOLYBDENUM ENZYME PROBABLE LONG GEPHYRIN DOMAIN Length = 146
#//
while (<CPGOUT>) { chomp; if (my ($id, $start, $end, $hid, $hstart, $hend, $score, $evalue) = /^(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+pd_(\S+);\S+\s+(\d+)\s+(\d+)\s+\S+\s+S=(\S+)\s+E=(\S+)/) { my $fp= $self->create_protein_feature($start,$end,$score,$id,$hstart,$hend,$hid,$self->analysis, sprintf("%.3e", $evalue),0); push @fps,$fp; } } close CPGOUT; $self->output(\@fps); } 1;
}
run_analysisdescriptionprevnextTop
sub run_analysis {
  my ($self) = @_;

  # run program
print STDERR "running ".$self->program." against ".$self->database."\n"; my @dbfiles = split(/;/,$self->analysis->db_file); # hmmm ... only the first bit is used
print STDERR "FILENAME: ".$self->queryfile."\n"; my $cmd = $self->program .' '. $self->options .' '. '-P ' . '/software/worm/iprscan/bin/binaries/blast/ ' . '-p ' . 'blastp' . ' '. '-d ' . $dbfiles[0] .' '. '-s ' . $self->queryfile . ' '. '-t ' . '/tmp' . ' '. '-h 0 -f '. ' >' . $self->resultsfile; print STDERR "$cmd\n"; $self->throw ("Error running ".$self->program." on ".$self->filename." against ".$dbfiles[0]) unless ((system ($cmd)) == 0);
}
General documentation
CONTACTTop
   Marc Sohrmann: ms2@sanger.ac.uk
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