changed  if ( defined $refseq_io ) to if ( !defined $refseq_io ), otherwise it
could not open the file

replaced 'shares_CDS_with' with two entries 'shares_CDS_with_ENST' and
'shares_CDS_with_OTTT'

message_only_once

script debugged and modified to produce gene, exon,transcript-and translation stable_ids
with correct prefixes . -start option modified !

be undefined.  Removes a whole lot of warnings when running with -w.

names "IMGT/GENE-DB" and in "IMGT/LIGM-DB".

Removed NOT NULL constraint on transcript.gene_id (should have been done when patch_41_42.sql was applied)

directory name as well as the file name, rather than $file, which
doesn't.

Use -d instead of -e to test for directories.

genes