[Biopython-dev] [Bug 2808] New: Bio.SeqIO "ig" format parser doesn't deal with optional 1 terminator

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2808

           Summary: Bio.SeqIO "ig" format parser doesn't deal with optional
                    1 terminator
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


While working on new unit test test_Emboss.py I noticed that EMBOSS seqret
creates ig files where the sequence includes a terminal digit one.  Further
research online suggests this is an optional feature of the file format,
although not commonly used.  See:
http://bmerc-www.bu.edu/needle-doc/latest/seq-formats.html#seq-file-format

The Bio.SeqIO "ig" parser should be aware of the (optional) terminal "1"
marker, and not include it in the returned sequence.  Perhaps we should even
add this when writing the files.


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