[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 #3 from biopython-bugzilla at maubp.freeserve.co.uk  2008-12-09 11:39 EST -------
(In reply to comment #2)
> If you remove the last two lines #------ from tmp_align.needle the program
> loops sucking more and more memory

You have an infinite loop, try modifying the bit near line 162 as follows:

        #Now should have the aligned query sequence with flanking region...
        while not (line.startswith(">") or ">>>" in line) and not
line.startswith('#'):
            match_seq_parts.append(line.strip())
            line = handle.readline()
            if not line :
                #End of file
                return None 

Also, your code is based on an out of date version of Bio/AlignIO/FastaIO.py -
probably from Biopython 1.47, and lacks improvements which may also apply to
the EMBOSS output.  Given the object orientated nature of the current m10
parser, you/we should be able to subclass it and only override those bit
dealing with the header and footer.  This is probably the nicest way forward if
we decide to treat the EMBOSS markx10 format as a new format in Bio.AlignIO.


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