[Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Nov 30 00:20:11 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2476





------- Comment #19 from maj at fortinbras.us  2008-11-30 00:20 EST -------
Created an attachment (id=1130)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1130&action=view)
HSPI.pm that uses 'native' subseq calls; fixed a mid-file 'use'

In HSPI.pm, subseq is called as subseq($beg,$end,'NATIVE') ( rearranged the
parm list to allow this shortcut, 
could also be ($beg,$end,1) ), which flags subseq() to do its tricky
gap/frameshift stuff. This works for the 2476 test case. 


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