The script has been updated accordingly.

 Now we loop through all the xrefs to find an xref of the type known/knownxref and not just the display_zref. Also the routine that moves xrefs form one ensembl object to another (e.g. from transcript to gene) has been rewritten as this was not behaving

added 2 new columns in the table: canonical_transcript_id and canonical_annotation and the respective methods in the API to get/set this new information

  my ( $current_start, $current_end );
as these variables were being declared twice

(If -outdir is not specified, or if the dir does not exist, then output from bjobs is written to pwd)

script for setting canonical transcript id in the gene table on the basis of simple rules

completely.