[Bioperl-l] AlignIO::stockholm write_aln()

Chris Fields cjfields at uiuc.edu
Mon Nov 6 11:35:52 EST 2006


I have added some experimental write_aln() support for Stockholm  
format to CVS along with some basic tests to AlignIO.t.  I plan on  
cleaning it up a bit and adding more tests, along with possibly  
adding a builder option (similar to SeqIO::genbank) to have  
annotation parsing optional.  Right now it is always on by default.

It doesn't print meta data yet but does parse and store it; I'll  
probably add that in the next day or two.

Be forewarned if testing this: I haven't tried clustal/msf/etc- 
 >stockholm conversions yet so don't know if that works, but it  
should (it just won't print annotations).  I'll add tests for that  
when I get time.

Chris

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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