[Biopython-dev] [Bug 2790] New: Genepop parser creates a full representation of the file on memory

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2790

           Summary: Genepop parser creates a full representation of the file
                    on memory
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: PopGen
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: tiagoantao at gmail.com


The genepop parser creates a full representation of the file on memory.

This is fine for most users (like with 100/200 individuals and 100 markers)
but, more and more people appear now with thousands of individuals and/or
thousands of loci. In some cases the whole file doesn't fit memory.

An alternative (iterator based) interface has to be created which only
maintains a subset of the file in memory


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