[Bioperl-guts-l] [Bug 2214] GenBank file parsing: version is 0 if name contains '-'

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Feb 21 11:10:59 EST 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2214





------- Comment #4 from cjfields at uiuc.edu  2007-02-21 11:10 EST -------
I believe we choose to primarily support a standard (INSDC databases or
UniProt, for instance) b/c:

1) it is much simpler to support, particularly for production purposes,  

2) it is much easier to deal with strict alphanumeric chars, particularly when
accessions parsed in other classes also rely on the same standard,

3) it wouldn't be valid GenBank/EMBL/UniProt format if it didn't use the
GenBank/EMBL/UniProt specs.

If you could point to a specific example where '-' or similar is used for
accessions in GenBank/EMBL/DDBJ I wouldn't have a problem adding this in.  I
can't see us supporting it otherwise.

Realize I am only one of the developers; others may disagree with me.  If you
want to press the point further, you are more than welcome to post to the
bioperl mail list:

http://bioperl.org/mailman/listinfo/bioperl-l

If you gather enough support for it we can reopen this and add in your patch. 
Don't be surprised, though, if this gets shot down by the other devs.


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