[Bioperl-guts-l] [Bug 2567] New: AlignIO::stockholm concatenates sequences

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2567

           Summary: AlignIO::stockholm concatenates sequences
           Product: BioPerl
           Version: 1.5 branch
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: bernd at bio.vu.nl


Hi,

This bug is related to 2042. Checked with the newest SVN version of today (15
aug 2008). Parsing stockholm alignments with the same sequence id results in
concatenation of these sequences. This problem mainly occurs with sequence
alignments from NCBI. No warning is raised for duplicates. Possibly a general
solution would be not to use the sequence id as hash key, but count the
sequence number within each block.

Attached is an example for the stockholm alignment.  gi|34978356  occurs twice
resulting in an alignment to of 100 instead of 50, and is_flush is false.


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