[Biopython-dev] [Bug 2808] New: Bio.SeqIO "ig" format parser doesn't deal with optional 1 terminator
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Wed Apr 8 18:55:59 EDT 2009
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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