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Issue #2643 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15421?detail_id=1795">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Migrated</i></li>
<li><strong>URL</strong> changed from <i>http://github.com/dalloliogm/biopython---popgen/tree/master/src/PopGen/Gio/fastPhaseOutputIO.py</i> to <i>https://github.com/biopython/biopython/issues/1726</i></li>
</ul>
<p>Migrated to GitHub as <a class="external" href="https://github.com/biopython/biopython/issues/1726">https://github.com/biopython/biopython/issues/1726</a></p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2643#change-15421">Bug #2643: Proposal: fastPhaseOutputIO for SeqIO</a></h1>
<ul><li>Author: Marco Dall'Olio</li>
<li>Status: Migrated</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: Not Applicable</li>
<li>URL: https://github.com/biopython/biopython/issues/1726</li></ul>
<p>Hi,<br />fastPHASE is software for haplotype reconstruction and missing genotype estimation from population genetic SNP data.<br />- <a class="external" href="http://stephenslab.uchicago.edu/software.html">http://stephenslab.uchicago.edu/software.html</a><br />It is commonly used by some population genetics bioinformaticians.</p>
<p>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.</p>
<p>fastPhase output contains information about SNPs and genotyping, and would probably be supported by the PopGen module that is being written for biopython.<br />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.<br />So, in the future we could have to fastPhaseOutputIterator-like modules, one that creates SeqRecord objects, and one other to be used in PopGen.</p>
<p>The module has been tested with doctest. I'll attach a file with the tests along with the module.</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1042/fastPhaseOutputIO.py">fastPhaseOutputIO.py</a>
(4.19 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1043/test_fastPhaseOutputIO.py">test_fastPhaseOutputIO.py</a>
(6.92 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1044/biopython_seqIO_fastPhaseOutputIO_patch">biopython_seqIO_fastPhaseOutputIO_patch</a>
(698 Bytes)<br />
<a href="https://redmine.open-bio.org/attachments/download/1046/fastPhaseOutputIO.py">fastPhaseOutputIO.py</a>
(5.44 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1047/test_fastPhaseOutputIO.py">test_fastPhaseOutputIO.py</a>
(6.47 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1048/fastphaseoutput">fastphaseoutput</a>
(1.82 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1050/fastPhaseOutputIO.py">fastPhaseOutputIO.py</a>
(5.39 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1051/test_fastPhaseOutputIO.py">test_fastPhaseOutputIO.py</a>
(6.85 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1053/fastPhaseTestFiles.zip">fastPhaseTestFiles.zip</a>
(2.67 KB)<br />
</fieldset>
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