[Biopython-dev] Martel stuff

Brad Chapman chapmanb at arches.uga.edu
Sat Sep 30 12:55:57 EDT 2000

Hey all;
	I have a few things relating to Martel:

1. I have a bit of a problem with something in the Clustalw parsing that
I just checked in (Bio/Clustalw/clustal_format.py). The newer clustalw
formatted files have these annoying starts that are in the file (I call
them match_stars in the format file). I just realized that these stars
aren't always there, so I made the following change to try and make them

--- clustal_format.py.orig	Thu Sep 28 19:49:37 2000
+++ clustal_format.py	Sat Sep 30 12:41:10 2000
@@ -59,7 +59,7 @@
 block_info = Martel.Group("block_info",
			   Martel.Rep(seq_line) +
-			   match_stars +
+			   Martel.MaxRepeat(match_stars, 0, 1) +
			   Martel.MaxRepeat(new_block, 0, 1))

I think this is right, but when I do this it makes the parse hang and
never finish. Hmmm.... I'm not sure how to debug this, any ideas?

2. I just installed 2.0b2, and it looks like we'll need the PyXML package
:-< Python2.0 doesn't seem to come with saxlib, which we need to
implement handler classes for the XML produced by Martel. The standard
xml library also doesn't have saxexts/sax2exts, and seems to have some
other differences from the PyXML package. Once the next version of PyXML
(0.6.1, I think) which is supposed to work with b2 comes out, I guess I
can see how well this works with what is in the standard library.
Anyways, I think this is the situation with python2.0. I'm not sure what
thoughts are about this...

3. What are people's thoughts about integrating Martel more tightly with
Biopython? Do you think it would be worthwhile for me to try my hand at
implementing a Martel based Fasta parser that would work with the code
Jeff has already got in place? 

Thanks for listening!


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