Raw content of Utils
<![CDATA[use strict;
use warnings;
package Utils;
use Exporter;
use Bio::EnsEMBL::Utils::Exception qw(info);
use vars qw(@ISA @EXPORT_OK);
@ISA = qw(Exporter);
@EXPORT_OK = qw(print_exon print_coords print_translation print_three_phase_translation);
#
# prints debugging info
#
sub print_exon {
my $exon = shift;
my $tr = shift;
if (!$exon) {
throw("Exon undefined");
}
info(" ".$exon->stable_id());
info(" cdna_start = ".$exon->cdna_start())
if(defined($exon->cdna_start()));
info(" cdna_end = ". $exon->cdna_end())
if(defined($exon->cdna_end()));
info(" start = ". $exon->start())
if(defined($exon->start()));
info(" end = ". $exon->end())
if(defined($exon->end()));
info(" strand = ". $exon->strand())
if(defined($exon->strand()));
if($exon->fail) {
info(" FAILED");
}
if($tr) {
info(" TRANSCRIPT:");
info(" cdna_coding_start = ". $tr->cdna_coding_start());
info(" cdna_coding_end = ". $tr->cdna_coding_end(). "\n");
}
return;
}
sub print_coords {
my $cs = shift;
foreach my $c (@$cs) {
if($c->isa('Bio::EnsEMBL::Mapper::Gap')) {
info(" GAP ". $c->length());
} else {
info(" ". $c->start. '-'. $c->end. ' ('.$c->strand.")");
}
}
}
sub print_translation {
my $tl = shift;
info("TRANSLATION");
if(!$tl) {
info(" undef");
return;
}
if($tl->start_Exon()) {
info(" start exon = ", $tl->start_Exon->stable_id());
} else {
info(" start exon = undef");
}
if($tl->end_Exon()) {
info(" end exon = ", $tl->end_Exon->stable_id);
} else {
info(" end exon = undef");
}
if(defined($tl->start())) {
info(" start = ", $tl->start());
} else {
info(" start = undef");
}
if(defined($tl->end())) {
info(" end = ", $tl->end());
} else {
info(" end = undef");
}
return;
}
sub print_three_phase_translation {
my $transcript = shift;
return if(!$transcript->translation());
my $orig_phase = $transcript->start_Exon->phase();
foreach my $phase (0,1,2) {
info("======== Phase $phase translation: ");
$transcript->start_Exon->phase($phase);
info("Peptide: " . $transcript->translate->seq() . "\n\n===============");
}
$transcript->start_Exon->phase($orig_phase);
return;
}
1;
]]>