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Issue #2704 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15412?detail_id=1772">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Closed</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>I'm going to close this due to lack of activity - hopefully we could parse the output from the later versions of EMBOSS.</p>
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<h1><a href="https://redmine.open-bio.org/issues/2704#change-15412">Bug #2704: Parser for the markx10 alignment format</a></h1>
<ul><li>Author: Osvaldo Zagordi</li>
<li>Status: Closed</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: </li></ul>
<p>Hi,<br />I recently wrote some code to parse the Emboss alignment format<br />markx10 (format explained at<br /><a class="external" href="http://emboss.sourceforge.net/docs/themes/AlignFormats.html">http://emboss.sourceforge.net/docs/themes/AlignFormats.html</a>)<br />Since it is slightly different from the Fasta m10 (not surprising, right?) I had to adapt FastaIO.py.<br />I thought this might eventually be included in biopython.<br />Important:<br />I noticed that if the alignment program exits for some reason and<br />does not close the alignment file with two lines like these<br />#---------------------------------------<br />#---------------------------------------<br />bad things can happen (e.g., sucking all the memory of the system)). <br />Could it be that a similar issue applies to FastaIO parser as well?<br />Best,<br /> Osvaldo</p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/1151/m10test.tgz">m10test.tgz</a>
(5.64 KB)<br />
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