[BioPython] blast output

[Douglas Kojetin]

Hi All-

A few questions ...

(1) RE:

 >I want to blast my sequence and get all possible results
 >If I run blast as in cookbook i get much more less results then
 >runnig blast manually and setting to 1000 the number of descriptions

 >How set the number of descrition NCBIWWW.qblast ???

I am also having difficulty setting the number of descriptions.  If I  
use the following command:

bresults = NCBIWWW.qblast('blastp', 'nr', seq, format_type='Text',  
alignments=0, descriptions=1000)

Only 100 results are output.  How can I increase the # of hits for a  
query?

(2) Is it possible to turn off this warning message?

WW.py:1062: UserWarning: qblast works only with blastn and blastp for  
now.
   warnings.warn("qblast works only with blastn and blastp for now.")

(3) I'd like to search the 'pdb' database for non-redundant protein  
structures.  If I do a 'nr' database search, it appears that non- 
redundant sequences for all databases (including the 'pdb') appear in  
the output.  Furthermore, the database name is the first line of the  
search (delimited by '|', pipe, character)

emb|...
pdb|...
gb|...

Is it possible to specify to search the 'nr' database and only output  
those hits from the 'pdb' database?  I know it would be easy to  
search the results of the query, using split('|') or line.find 
('pdb'), but I'm not getting enough hits from the 'pdb' database  
during the 'nr' query (related to my question 1 above).


Many thanks in advance for your help,
Doug