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Issue #2819 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15419?detail_id=1790">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Migrated</i></li>
<li><strong>URL</strong> set to <i>https://github.com/biopython/biopython/issues/1725</i></li>
</ul>
<p>Migrated to GitHub as <a class="external" href="https://github.com/biopython/biopython/issues/1725">https://github.com/biopython/biopython/issues/1725</a></p>
<hr />
<h1><a href="https://redmine.open-bio.org/issues/2819#change-15419">Bug #2819: Bio.SeqIO support for NCBI protein tables (*.ptt files)</a></h1>
<ul><li>Author: Peter Cock</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/1725</li></ul>
<p>On their FTP site the NCBI provide a range of files for each genome/plasmid/chromosome, e.g.<br /><a class="external" href="ftp://ftp.ncbi.nih.gov/genomes/Protozoa/Cryptosporidium_parvum/">ftp://ftp.ncbi.nih.gov/genomes/Protozoa/Cryptosporidium_parvum/</a></p>
<p>The *.ptt files are simple tab separated tables listing all the proteins. They correspond to the CDS features in the GenBank file.</p>
<p>This enhancement bug is about adding "ptt" as an input file format in Bio.SeqIO (and potentially as an output format too), where a single ptt file gives a single SeqRecord object containing a SeqFeature object for each protein. The header line gives the sequence length, so an UnknownSeq can be used for the SeqRecrd's seq property.</p>
<p>One example application of this would be to draw a GenomeDiagram showing the protein locations. This can be done using the SeqFeature objects from parsing a GenBank file, but using the ptt file will be much faster.</p>
<p>See earlier suggestions on the mailing list (part of the GFF thread):<br /><a class="external" href="http://lists.open-bio.org/pipermail/biopython-dev/2009-April/005725.html">http://lists.open-bio.org/pipermail/biopython-dev/2009-April/005725.html</a><br /><a class="external" href="http://lists.open-bio.org/pipermail/biopython-dev/2009-April/005745.html">http://lists.open-bio.org/pipermail/biopython-dev/2009-April/005745.html</a></p>
<p>Patch to follow...</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1282/ProteinTableIO.py">ProteinTableIO.py</a>
(8.12 KB)<br />
<a href="https://redmine.open-bio.org/attachments/download/1283/add_ptt.patch">add_ptt.patch</a>
(486 Bytes)<br />
<a href="https://redmine.open-bio.org/attachments/download/1284/test_ptt.patch">test_ptt.patch</a>
(957 Bytes)<br />
</fieldset>
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