[Biopython-dev] [Bug 2557] New: AlignIO::write fails when delegating to SeqIO::write

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2557

           Summary: AlignIO::write fails when delegating to SeqIO::write
           Product: Biopython
           Version: 1.47
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: rsuri at cs.utexas.edu


In line 185 of "biopython/Bio/AlignIO/__init__.py" in the current CVS version,
there's a call to SeqIO::write with only 2 arguments instead of the required 3
["SeqIO.write(alignment.get_all_seqs(), format)"] should be
["SeqIO.write(alignment.get_all_seqs(), handle, format)"] (i.e. pass the handle
object).  

I know this happens when trying to output to FASTA format, and it appears to do
so more generally whenever the SeqIO module can be used for output.


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