[Biopython-dev] Documentation for new Blast parser

[Michiel Jan Laurens de Hoon]

Thanks, Peter! These are all good points. I've updated the tutorial 
following your suggestions.

Peter wrote:
>> For the upcoming Biopython release, I rewrote the chapter on Blast in 
>> the tutorial to describe our new Blast parser. For those of you who 
>> want to have a preview, I put a copy here:
>>
>> http://biopython.org/DIST/docs/tutorial/Tutorial-new.html
 >
 > 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.

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

> --------------------------------------------------------------------
> 
> In section "3.1  Running BLAST locally" the wording about the location 
> of the database files could be a little clearer.
> 
> You wrote the following (which I have reformatted to use shorter lines):
> 
>  >>> my_blast_db = "/home/mdehoon/Data/Genomes/Databases/bsubtilis"
> # I used formatdb to create a BLAST database named bsubtilis in the
> # directory /home/mdehoon/Data/Genomes/Databases.
> # The BLAST database consists of the files bsubtilis.nhr, bsubtilis.nin,
> # and bsubtilis.nsq in this directory.
> 
> You talk about four files, but only name three of them.

There are only three files, so maybe my description is confusing and 
suggests that there should be four files. I've updated the Tutorial to 
show the full path of the three files.

> Also should it be "Biopython" or "BioPython"?  The website uses a 
> mixture...

A long time ago it was decided that "Biopython" is the official name. 
Though BioPython and biopython also appear all over the place.

Thanks again, Peter.

--Michiel


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