Bio::EnsEMBL::Analysis::Runnable BestTargettedExonerate
Other packages in the module: Bio::EnsEMBL::Analysis::Runnable::BestTargetted
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Package variables
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Included modules
Bio::EnsEMBL::Analysis::Runnable::BaseExonerate
Inherit
Bio::EnsEMBL::Analysis::Runnable::BaseExonerate
Synopsis
No synopsis!
Description
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Methods
parse_results
No description
Code
query_type
No description
Code
target_type
No description
Code
Methods description
None available.
Methods code
parse_resultsdescriptionprevnextTop
sub parse_results {
  my ($self, $fh) = @_;

  my $score = 0;
  my $perc_id = 0;
  
  # my $basic_options = "--showsugar false --showvulgar false --showalignment false --ryo \"RESULT: %S %pi %ql %tl %g %V\\n\" ";
while (<$fh>){ if ($_=~/^RESULT:/){ my @tmp = split/\s+/, $_; print "exonerate results @tmp "; print "\n"; # my (
# $tag, $q_id, $q_start, $q_end, $q_strand,
# $t_id, $t_start, $t_end, $t_strand, $score,
# $perc_id, $q_length, $t_length, $gene_orientation,
# @vulgar_blocks
# ) = split;
# my($match_type, $query_match_length, $target_match_length,@rest_of_vulgar) = @vulgar_blocks;
if ($score < $tmp[9]){ $score = $tmp[9]; #return the best score
$perc_id = $tmp[10]; } } } $self->output([$score, $perc_id]); } 1;
}
query_typedescriptionprevnextTop
sub query_type {
  my ($self) = @_;
  
  return 'protein';
}
target_typedescriptionprevnextTop
sub target_type {
  my ($self) = @_;

  return 'protein';
}
General documentation
No general documentation available.