[Biopython-dev] [Biopython (old issues only) - Bug #2704] (Closed) Parser for the markx10 alignment format

[redmine at redmine.open-bio.org]

Issue #2704 has been updated by Peter Cock.

Description updated
Status changed from New to Closed
% Done changed from 0 to 100

I'm going to close this due to lack of activity - hopefully we could parse the output from the later versions of EMBOSS.

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Bug #2704: Parser for the markx10 alignment format
https://redmine.open-bio.org/issues/2704#change-15412

* Author: Osvaldo Zagordi
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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Hi,
I recently wrote some code to parse the Emboss alignment format
markx10 (format explained at
http://emboss.sourceforge.net/docs/themes/AlignFormats.html)
Since it is slightly different from the Fasta m10 (not surprising, right?) I had to adapt FastaIO.py.
I thought this might eventually be included in biopython.
Important:
I noticed that if the alignment program exits for some reason and
does not close the alignment file with two lines like these
#---------------------------------------
#---------------------------------------
bad things can happen (e.g., sucking all the memory of the system)). 
Could it be that a similar issue applies to FastaIO parser as well?
Best,
        Osvaldo

---Files--------------------------------
m10test.tgz (5.64 KB)


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