[Biopython-dev] [Bug 2999] New: SeqIO.parse() or record.format("genbank") converts input sequence to uppercase or

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2999

           Summary: SeqIO.parse() or record.format("genbank") converts input
                    sequence to uppercase or
           Product: Biopython
           Version: 1.53
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mmokrejs at ribosome.natur.cuni.cz


I do not know where is the problem coming from but if I parse a GenBank file
with lowercased sequence (EST) and get it printed back through
record.format("genbank") I receive all in uppercase. I think the
upper/lower-casing should never be altered unless explicitly requested by the
user.

for _record in SeqIO.parse(_infile, options.format):
    # silly, imagine I hit "gi|14150838|gb|AAK54648.1|AF376133_1" from
    #   a FASTA file :(
    if _record.id in _ids:
        _outfile.write(_record.format("fasta"))
    elif options.format == "genbank":
        if _record.annotations['gi'] in _ids:
            _outfile.write(_record.format("genbank"))


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