[Biopython-dev] [Biopython (old issues only) - Bug #2643] (Migrated) Proposal: fastPhaseOutputIO for SeqIO

[redmine at redmine.open-bio.org]

Issue #2643 has been updated by Peter Cock.

Description updated
Status changed from New to Migrated
URL changed from http://github.com/dalloliogm/biopython---popgen/tree/master/src/PopGen/Gio/fastPhaseOutputIO.py to https://github.com/biopython/biopython/issues/1726

Migrated to GitHub as https://github.com/biopython/biopython/issues/1726

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Bug #2643: Proposal: fastPhaseOutputIO for SeqIO
https://redmine.open-bio.org/issues/2643#change-15421

* Author: Marco Dall'Olio
* Status: Migrated
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: https://github.com/biopython/biopython/issues/1726
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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.

---Files--------------------------------
fastPhaseOutputIO.py (4.19 KB)
test_fastPhaseOutputIO.py (6.92 KB)
biopython_seqIO_fastPhaseOutputIO_patch (698 Bytes)
fastPhaseOutputIO.py (5.44 KB)
test_fastPhaseOutputIO.py (6.47 KB)
fastphaseoutput (1.82 KB)
fastPhaseOutputIO.py (5.39 KB)
test_fastPhaseOutputIO.py (6.85 KB)
fastPhaseTestFiles.zip (2.67 KB)


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