[Bioperl-l] GeneStructure

Hilmar Lapp hilmarl@yahoo.com
Sun, 11 Feb 2001 21:58:17 -0800

I finished the implementation of ExonI and TranscriptI in Exon.pm
and Transcript.pm, respectively, all in Bio/SeqFeature/Gene.

Both took an unexpected amount of coding, expecially Transcript,
but they should be fairly generic now. Please review the code.

In particular, I added is_coding() to ExonI. mrna() in TranscriptI
does not make much sense in my opinion, it calls for inconsistent
and unexpected behaviour (what do you do with the promoter, what
if the UTR features haven't been typed to 5' or 3', etc). cds()
should be sufficient, but I'm not sure.

The GeneStructureI implementation shouldn't be much remaining
work, because Transcript.pm takes over most of the more difficult

Unfortunately, since Friday night I have been unable to establish
a CVS connection (I wrote to root-l), so until this is fixed you
won't see any of the files or changes.

Regarding the deadline, I'm sorry that this has to be delayed
further, but BioPerl presently is a spare-time only enjoyment, and
this weekend not even this. I expect the freeze call to happen on
Tuesday night at the latest.

Hilmar Lapp                              email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757