moved some debugging aid functions into Utils module

misc-scripts/chimp/Utils.pm

+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);
+
+
+
+#
+# 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");
+    } 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;
+}
+
+
+1;