[Biopython-dev] [Bug 2704] Parser for the markx10 alignment format

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2704





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-12-09 10:35 EST -------
This sounds interesting Osvaldo,

Now that you've filed this bug, you should be able to upload the python file
(or a patch).

Given EMBOSS's markx10 output is intended to be like FASTA's -m 10 output (but
with the addition of EMBOSS style headers and footers), it *might* be nicer to
have one parser for both.  Right now I don't know how similar EMBOSS's output
really is.

If we do go for the simpler option of two separate parsers, it would certainly
be a good idea in the long run for them to share some code.

(In reply to comment #0)
> 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?

Does this happen create such a file by hand (lacking these files) and try and
read that?  If so it should be easier to debug.

Peter


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.