[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
Tue Dec 16 16:15:25 EST 2008


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





------- Comment #30 from maj at fortinbras.us  2008-12-16 16:15 EST -------
(In reply to comment #29)
> Mark, latest patch to LocatableSeq is giving tons of warnings and some failed
> tests.  I want to add this in but the timeline is working against us on this
> one, so I'm pushing it to a later release.  Not sure but I think there is some
> overly recursive behavior going on.  Make sure you have 'use strict; use
> warnings' for code, I had over 100000 lines of the following warning or
> similar:
> 
> Use of uninitialized value $rplc_rt in concatenation (.) or string at
> Bio/LocatableSeq.pm line 959, <GEN0> line 101.
> Use of uninitialized value $rplc in concatenation (.) or string at
> Bio/LocatableSeq.pm line 926, <GEN0> line 101.
> Use of uninitialized value $rplc_lf in concatenation (.) or string at
> Bio/LocatableSeq.pm line 959, <GEN0> line 101.
> Use of uninitialized value $rplc_rt in concatenation (.) or string at
> Bio/LocatableSeq.pm line 959, <GEN0> line 101.
> Use of uninitialized value $rplc in concatenation (.) or string at
> Bio/LocatableSeq.pm line 926, <GEN0> line 101.
> Use of uninitialized value $rplc_lf in concatenation (.) or string at
> Bio/LocatableSeq.pm line 959, <GEN0> line 101.
> Use of uninitialized value $rplc_rt in concatenation (.) or string at
> Bio/LocatableSeq.pm line 959, <GEN0> line 101.
> 
Ugh, Chris-terrible. Sorry-will use warnings.


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