[Biopython-dev] Documentation for new Blast parser

[Peter]

Michiel Jan Laurens de Hoon wrote:
> Thanks, Peter! These are all good points. I've updated the tutorial 
> following your suggestions.

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"?

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.

Link to ViewCVS if anyone is interested:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Doc/Tutorial.tex?cvsroot=biopython

I presume you run some flavour of latex to html on it, and then upload 
the file to website somehow...

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Back to the BLAST tutorial, quoting Section 3.1  Running BLAST locally:

> Running BLAST locally (as opposed to over the internet, see Section
> 3.2) has two advantages:
> 
> * Local BLAST may be faster than BLAST over the internet;
> 
> * Local BLAST allows you to make your own database to search for
> sequences against.
> 
> * Dealing with proprietary or unpublished sequence data can be
> another reason to run BLAST locally. You may not be allowed to
> redistribute the sequences, so submitting them to the NCBI as a BLAST
> query would not be an option.

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point for the proprietary/unpublished data paragraph.

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> Peter wrote:
>> I am wondering if now is a good time to switch the default output 
>> format to XML in NCBIStandalone.blastall, NCBIStandalone.rpsblast
>> etc given  NCBIWWW.qblast already defaults to XML.

Michiel wrote:
> I agree that these functions should return XML by default.
> Objections, anybody? If not, I'll make this change and update the
> tutorial accordingly.

It will catch a few people out, but it seems best to do it now at the 
same time as the related Blast XML changes.  Do the HTML and Text 
parsers spot when they are fed XML input, and give a helpful error message?

Should we also mention this change in the DEPRECATED file?

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/DEPRECATED?cvsroot=biopython

Peter