Raw content of Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Superfamily_wormbase
<![CDATA[package Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Superfamily_wormbase;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation;
@ISA = qw(Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation);
###################
# analysis methods
###################
=head2 run_program
Title : run_program
Usage : $self->program
Function : makes the system call to program
Example :
Returns :
Args :
Throws :
=cut
sub run_analysis {
my ($self) = @_;
# run program
print STDERR "running ".$self->program." against ".$self->queryfile."\n";
print STDERR "FILENAME: ".$self->queryfile."\n";
my $cmd = $self->program .' '.
$self->analysis->parameters .' '.
'-i ' . $self->queryfile.' '.
'-o ' . $self->resultsfile;
print STDERR "$cmd\n";
$self->throw ("Error running Superfamily_wormbase ".$self->program." on ".$self->filename)
unless ((system ($cmd)) == 0);
}
=head2 parse_results
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 :
=cut
sub parse_results {
my ($self) = @_;
my $filehandle;
my $resfile = $self->resultsfile();
my @fps;
if (-e $resfile) {
if (-z $resfile) {
print STDERR "Superfamily didn't find any hits\n";
return;
} else {
open (CPGOUT, "<$resfile") or $self->throw("Error opening ", $resfile, " \n"); #
}
}
# example output lines:
#R186.4 63882 0019507 9 181 2.6e-37 msssgllkPATLDDVFQKLEDLCKLFpPQEKTVNVTSLkTGRILAEDIITEYDIPAQRTSIVDGFAIIVNQLGTKREIVGLSTAVTPYNAELISNECVRITIGGVVPDGADTVVPIENVALlkEEKCIEVLRKPKEGDNIREVGSEAKTGEILLKDGHHLDTMSITLLHALGISQVEIYKKprvcvlsigsdlnsnkmygsfnrsqllelfqsqgftaidagsstehiteveekirtaasfacvlvtvggaqvirevaktlkfkfeiqdvdstpgnftvstgkidetpvvlsifpeyhvsswiganlfvspilramegqnsetshrfkaeltqpisktsetrflrarsevskgnlistplgcedifgansilevksntcfsagdvvdlrfa Molybdenum cofactor biosynthesis protein MoeA, N-terminal and linker domains
#//
#R186.4 53218 0017938 180 353 3.9e-14 msssgllkpatlddvfqkledlcklfppqektvnvtslktgrilaediiteydipaqrtsivdgfaiivnqlgtkreivglstavtpynaelisnecvritiggvvpdgadtvvpienvallkeekcievlrkpkegdnirevgseaktgeillkdghhldtmsitllhalgisqveiyKKPRVCVLSIGSDLNSNKMYgSFNRSQLLELFQSQGFTAIDAGSSTEHITEVEEKIRTAASFACVLVTVGGAQVIREVAKTLKFKFEIQDVDSTPGNFTVSTGKIDetPVVLSIFPEYHVSSWIGANLFVSPILRAMEGQNSETSHRFKAELTQPISKTSETRFLRARSEVSKGnlistplgcedifgansilevksntcfsagdvvdlrfa Molybdenum cofactor biosynthesis proteins
#//
my $id;
while (<CPGOUT>) {
chomp;
next if (/^\/\//);
print "$_\n";
if (my ($id, $hid, $start, $end, $evalue) = /^(\S+)\s+(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+(\S+)/) {
print "matched\n";
my $score = 0;
my $hstart = 0;
my $hend = 0;
my $hid = "SSF$hid";
my $percentIdentity = 0;
$evalue *= 1; # force evalue to be a float not a string
print "output= $start, $end, $score, $id, $hstart, $hend, $hid, $self->analysis, $evalue, $percentIdentity\n";
my $fp= $self->create_protein_feature($start, $end, $score, $id, $hstart, $hend, $hid, $self->analysis, $evalue, $percentIdentity);
push @fps, $fp;
}
}
close (CPGOUT);
$self->output(\@fps);
for ( @fps ) {
print "value : " . $_->p_value() . "\n" ;
}
}
1;
]]>