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

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

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

           Summary: Parser for the markx10 alignment format
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: osvaldo.zagordi at bsse.ethz.ch


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


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