[Biopython-dev] Documentation for new Blast parser

Michiel Jan Laurens de Hoon mdehoon at c2b2.columbia.edu
Sun Mar 11 02:40:26 UTC 2007

Peter wrote:
> I see you have started to mention Bio.SeqIO in the Blast documentation - 
> is this a hint to get me to update section 2.4  "Parsing biological file 
> formats"?

If you could do that, then that would be great. If you don't find the 
time for it, I can also help you by grabbing what you have on your wiki 
page. Feel free to change section 2.4 as you want -- I don't think 
what's there is still very relevant to Biopython, and it probably scares 
people off.

> I see you are editing the CVS file biopython/Doc/Tutorial.tex - I am 
> happy working with LaTex so that shouldn't be a problem.

Note that it is not exactly LaTeX, but LaTeX with hevea added. Let me 
know if you run into problems with hevea.
> I presume you run some flavour of latex to html on it, and then upload 
> the file to website somehow...

Hevea takes care of this; see the Makefile in biopython/Doc.

> Back to the BLAST tutorial, quoting Section 3.1  Running BLAST locally:
> Minor style point: Using the bullet points makes it look like three 
> advantages (when the introduction says two).  I wouldn't use a bullet 
> point for the proprietary/unpublished data paragraph.

Ha, you're right. I should work on my counting skills.

It's fixed now.

Thanks again,


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032

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