[Bioperl-l] CDS complement statements from GenBank

Galeb Abu-Ali abualiga at gmail.com
Sun Mar 27 09:34:05 EDT 2011


I'm trying to parse CDS complement statements from GenBank files of
bacterial genomes. I know it works for 'join' statements with
Bio::Location::SplitLocationI, but there is no spliced genes in
bacterial annotations and therefore no 'join()' statements. When I
replace 'complement' with 'join' in the bacterial GenBank file,
Bio::Location::SplitLocationI gets the coordinates. I took a look at
SplitLocationI.pm and Split.pm to see if I could replace 'join' with
'complement' to get it to work but no luck. At your convenience,
please advise.



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