[Biopython-dev] [Bug 2227] New: Writing Nexus files with Bio.SeqIO

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat Mar 10 20:32:15 UTC 2007


           Summary: Writing Nexus files with Bio.SeqIO
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk

I would like to be able to write multiple sequence alignments in Nexus format,
using Bio.SeqIO (and possibly also Bio.Nexus).

I have tried to do this by creating a nexus object in code (from an existing
alignment) using the add_sequence() method, with the intention of then calling
its write_nexus_data() method.

However, it seems that add_sequence() is intended for use when the alignment
matrix has already been created - not for building one from scratch.

I will attached code for Bio.SeqIO to write a Nexus alignment WITHOUT using
Bio.Nexus, which seemed easier.

I would prefer to use Bio.Nexus to do this however...

[This issue can wait till after we release BioPython 1.43]

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