[Biopython-dev] [Bug 2643] New: Proposal: fastPhaseOutputIO for SeqIO

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2643

           Summary: Proposal: fastPhaseOutputIO for SeqIO
           Product: Biopython
           Version: Not Applicable
          Platform: PC
               URL: http://github.com/dalloliogm/biopython---
                    popgen/tree/master/src/PopGen/Gio/fastPhaseOutputIO.py
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: dalloliogm at gmail.com
                CC: tiagoantao at gmail.com


Hi,
fastPHASE is software for haplotype reconstruction and missing genotype
estimation from population genetic SNP data.
- http://stephenslab.uchicago.edu/software.html
It is commonly used by some population genetics bioinformaticians.

I had to convert the output from a fastPhase run to fasta; so I wrote a module
that reads a fastPhase output file, and returns SeqRecord objects.

fastPhase output contains information about SNPs and genotyping, and would
probably be supported by the PopGen module that is being written for biopython.
However, my module is thought to be used only to read the sequence information
from the output file, and to create SeqRecord objects, ignoring any other kind
of information.
So, in the future we could have to fastPhaseOutputIterator-like modules, one
that creates SeqRecord objects, and one other to be used in PopGen.

The module has been tested with doctest. I'll attach a file with the tests
along with the module.


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