[Biopython-dev] [Bug 1920] New: Bio.Geo does not support recent GEO files

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1920

           Summary: Bio.Geo does not support recent GEO files
           Product: Biopython
           Version: Not Applicable
          Platform: PC
               URL: http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html
                    #SOFTformat
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Martel/Mindy
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


The NCBI tweaked their GEO SOFT file format this year (2005) and the old
Bio.Geo parser can't cope.

I have fixed the Martel format definition to support this (and the old test
cases).

I have also changed the Geo.Iterator as it didn't seem to work (it seemed to be
doing an entire file at a time).

Patch to follow, along with new test cases from the NCBI.




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