[Bioperl-guts-l] [Bug 2930] New: Bio::PrimarySeqI::translate hardcoded test for '*' as terminator

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Oct 19 07:02:00 EDT 2009


http://bugzilla.open-bio.org/show_bug.cgi?id=2930

           Summary: Bio::PrimarySeqI::translate hardcoded test for '*' as
                    terminator
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: asjo at koldfront.dk


Bio::PrimarySeqI::translate allows the caller to give a -terminator option,
specifying the terminator character - the default is '*'.

translate also has a check that there are no *'s in the translated sequence. It
looks like it ought to look for $terminator instead?

Patch including test attached.


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