Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation IPRScan
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Package variables
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Included modules
Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Inherit
Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation
Synopsis
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Description
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Methods
multiprotein
No description
Code
new
No description
Code
parse_results
No description
Code
run_analysis
No description
Code
Methods description
None available.
Methods code
multiproteindescriptionprevnextTop
sub multiprotein {
  my ($self) = @_;
  return 1;
}


##################
}
newdescriptionprevnextTop
sub new {
  my ($class, @args) = @_;
  my $self = $class->SUPER::new(@args);
  
  ######################
#SETTING THE DEFAULTS#
######################
$self->options('-cli -appl blastprodom -appl fprintscan -appl hmmpfam -appl superfamily -appl hmmpir -appl scanregexp -format raw') if(!$self->options); #$self->options('-cli -appl blastprodom -appl fprintscan -appl hmmpfam -appl hmmpir -appl hmmpanther -appl hmmtigr -appl hmmsmart -appl superfamily -format raw') if(!$self->options);
#self->options('-cli -appl blastprodom -appl fprintscan -appl hmmpfam -appl hmmpir -appl hmmpanther -appl hmmtigr -appl hmmsmart -appl superfamily -appl gene3d -format raw')
######################
return $self; } #testing the different programs
# -appl <name> Application(s) to run (optional), default is all.
# Possible values (dependent on set-up):
# * blastprodom
# * fprintscan
# 8 hmmpfam
# 8 hmmpir
# * hmmpanther
# 8 hmmtigr
# 7 hmmsmart
# 8 superfamily
# * gene3d
# 8 scanregexp
# 8 profilescan
# 8 seg
# 8 coils
# 8 [tmhmm]
# 8 [signalp]
#################
}
parse_resultsdescriptionprevnextTop
sub parse_results {
  my ($self) =  @_;
  print "PARSING RESULTS\n";
  open(OUT, "<".$self->resultsfile) or throw("FAILED to open ".
                                             $self->resultsfile.
                                             " IPRSCAN:parse_results");
  my @out;
  while(<OUT>){
    print;
    chomp;
    if(/SUBMITTED\s+(\S+)/){
      my $dir_name = $1;
      #print "GETTING filename HAVE ".$dir_name."\n";
#iprscan-20071115-10500980
my ($base_dir) = $dir_name =~ /iprscan\-(\d+)\-\d+/; my $full_path = $self->workdir."/".$base_dir."/".$dir_name; $self->files_to_delete($full_path); #print $full_path."\n";
next; } next if((!$_) || (!$_ =~ /\d+/)); #print $_."\n";
#19897 4AB50DD3FDE96DB6 468 ProfileScan PS50157 ZINC_FINGER_C2H2_2 243 270 16.685 T 14-Nov-2007
my ($translation_id, $crd, $aa_length, $method, $hit_name, $desc, $start, $end, $evalue, $status, $date) = split /\t/, $_; if(!$start || !$end){ next; } if($evalue && !($evalue =~ /\d+/)){ $evalue = undef; } if($start > $end){ my $temp = $start; $start = $end; $end = $temp; } my $pf = $self->create_protein_feature($start, $end, 0, $translation_id, 0, 0, $hit_name, $self->analysis, $evalue, 0); throw("Protein feature has no translation id") if(!$pf->seqname); push(@out, $pf); } $self->output(\@out); close(OUT); } #NF00181542 is the id of the input sequence.
#27A9BBAC0587AB84 is the crc64 (checksum) of the protein sequence (supposed to be unique).
#272 is the length of the sequence (in AA).
#HMMPIR is the anaysis method launched.
#PIRSF001424 is the database members entry for this match.
#Prephenate dehydratase is the database member description for the entry.
#1 is the start of the domain match.
#270 is the end of the domain match.
#6.5e-141 is the evalue of the match (reported by member database anayling method).
#T is the status of the match (T: true, M: marginal).
#06-Aug-2005 is the date of the run.
}
run_analysisdescriptionprevnextTop
sub run_analysis {
  my ($self) = @_;
  #example command
#/nfs/acari/lec/code/interpro/interpro_ftp/iprscan/bin/iprscan -cli -format raw
#-i /nfs/acari/lec/code/interpro/interpro_ftp/iprscan/test.seq
print "RUNNING ANALYSIS\n"; my $command = $self->program." ".$self->options." -i ".$self->queryfile. " >& ".$self->resultsfile; print "Running ".$command."\n"; throw ("Error running ".$command)unless ((system ($command)) == 0);
}
General documentation
No general documentation available.