helper module to keep track of types of mapping failures

misc-scripts/chimp/ErrCode.pm

+use strict;
+use warnings;
+
+package ErrCode;
+
+use Exporter;
+
+use vars qw(@EXPORT_OK @ISA);
+
+@ISA = qw(Exporter);
+
+@EXPORT_OK = qw(&set_err &get_err &ec2str);
+
+
+use constant OK => 0;
+
+use constant PART_EXON_CDS_DELETE_TOO_LONG             => 1;
+use constant PART_EXON_CDS_FRAMESHIFT_DELETE_TOO_LONG  => 2;
+use constant PART_EXON_CDS_DELETE_ENTIRE               => 3;
+use constant PART_EXON_CDS_INSERT_TOO_LONG             => 4;
+use constant PART_EXON_CDS_FRAMESHIFT_INSERT_TOO_LONG  => 5;
+use constant PART_EXON_CONFUSED                        => 6;
+
+use constant NO_CDS_LEFT => 7;
+
+use constant EXON_DELETE_CODING => 10;
+use constant EXON_STRAND_FLIP   => 11;
+use constant EXON_INVERT        => 12;
+use constant EXON_SCAFFOLD_SPAN => 13;
+
+use constant TRANSCRIPT_STRAND_FLIP   => 20;
+use constant TRANSCRIPT_INVERT        => 21;
+use constant TRANSCRIPT_SCAFFOLD_SPAN => 22;
+
+use constant TRANSCRIPT_DOES_NOT_TRANSLATE => 30;
+
+
+my $ERR;
+
+sub  set_err {
+  $ERR = shift;
+}
+
+sub get_err {
+  my $cur_err = $ERR;
+  $ERR = OK;
+  return $cur_err;
+}
+
+
+#converts an error code to a string
+sub ec2str {
+  my $ec = shift;
+
+  my $str = '';
+
+  if($ec == OK) {
+    $str = 'OK';
+  }
+  elsif($ec == PART_EXON_CDS_DELETE_TOO_LONG) {
+    $str =  'Exon CDS deletion too long.';
+  }
+  elsif($ec == PART_EXON_CDS_FRAMESHIFT_DELETE_TOO_LONG) {
+    $str = 'Exon frameshifting deletion too long.';
+  }
+  elsif($ec == PART_EXON_CDS_DELETE_ENTIRE) {
+    $str = 'Entire CDS deleteion.';
+  }
+  elsif($ec == PART_EXON_CDS_INSERT_TOO_LONG) {
+    $str = 'Exon CDS insertion too long.';
+  }
+  elsif($ec == PART_EXON_CDS_FRAMESHIFT_INSERT_TOO_LONG) {
+    $str = 'Exon frameshifting insertion too long.';
+  }
+  elsif($ec == NO_CDS_LEFT) {
+    $str = 'No CDS left following CDS adjustments due to inserts/deletions';
+  }
+  elsif($ec == PART_EXON_CONFUSED) {
+    $str = 'Confused due to insert following short match consumed ' .
+      'by introduced frameshift intron.';
+  }
+  elsif($ec == EXON_DELETE_CODING) {
+    $str = 'Entire coding exon deletion.';
+  }
+  elsif($ec == EXON_STRAND_FLIP) {
+    $str = 'Exon flips strands.';
+  }
+  elsif($ec == EXON_INVERT) {
+    $str = 'Exon inversion.';
+  }
+  elsif($ec == EXON_SCAFFOLD_SPAN) {
+    $str = 'Exon spans multiple scaffolds.';
+  }
+  elsif($ec == TRANSCRIPT_STRAND_FLIP) {
+    $str = 'Transcript flips strands.';
+  }
+  elsif($ec == TRANSCRIPT_INVERT) {
+    $str = 'Transcript inversion.';
+  }
+  elsif($ec == TRANSCRIPT_SCAFFOLD_SPAN) {
+    $str = 'Transcript spans multiple scaffolds.';
+  }
+
+  return $str;
+}
+
+1;