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

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





------- Comment #9 from dalloliogm at gmail.com  2008-11-06 11:12 EST -------
(In reply to comment #7)
> I've now had a quick look at the fastPHASE documentation, and I have the
> impression that the sequences should always come in pairs:

right!

> "Output files for inferred haplotypes or imputed genotypes contain two lines 
> per given diploid individual, with the order of individuals corresponding to 
> that supplied in the input file."
> 
> Assuming the paired sequences are always the same length, this does suggest the
> format should be integrated into Bio.AlignIO (giving pairwise alignments)
> rather than Bio.SeqIO.



> Have you tried not estimating the haplotypes (by supplying a negative integer
> following -H), and does this alter the sequence output?

I will try it, ok.

> Finally could you try the -Z command line argument for the simplified output
> format (described as two lines per individual, without “id” lines,
> subpopulation labels or summary information from the run).  Does this have the
> sequences?  If so this may be a more parser friendly set of output to parse for
> Bio.SeqIO and/or Bio.AlignIO.

ok, I can try to implement both of the two formats, but for the moment I will
prefer to concetrate on one.


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