[Bioperl-guts-l] [Bug 2165] Bio::SeqIO does not write correct taxonomy data in SwissProt format

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2165





------- Comment #5 from cjfields at uiuc.edu  2007-09-02 22:33 EST -------
(In reply to comment #3)
> Hi Chris,
> 
> ...
> Still, the formatting should (imho) be corrected; the specs of SwissProt do not
> exclude the presence of "OS" alone (i.e. without "OC").


Note the table located here (after the sample record):

http://ca.expasy.org/sprot/userman.html#entrystruc

excerpt: 
...
GN      Gene name(s)             Optional
OS      Organism species         Once
OG      Organelle                Optional
OC      Organism classification  Once or more
...

The OS/OC lines are not 'optional'.  As mentioned before, any organism with a
common_name() should be accompanied by a valid scientific_name() or it isn't a
completely valid Bio::Species object.

We'll consider adding an exception/warning to the various write_seq() methods
if an incomplete Bio::Species is used, but we won't fix output (GIGO applies
here).


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.