[Biopython-dev] [Bug 2408] New: GenBank records do not contain U's

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2408

           Summary: GenBank records do not contain U's
           Product: Biopython
           Version: 1.43
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: marcin.cieslik at gmail.com


The GenBank GenBank.FeatureParser() assigns a wrong alphabet for ss-RNA
records:

all GenBank records use T's not U's:
http://www.bioperl.org/pipermail/bioperl-l/2001-October/006400.html

parsing of:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=511859

results in:
u'511859': SeqRecord(seq=Seq('CAC  <<CUT>>  TGG', IUPACAmbiguousRNA()),
id='M23021.1', name='MSBMVCCG', description='Southern cowpea mosaic virus,
complete genome.', dbxrefs=[])}


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