[BioPython] Problems with NCBIXML.py

[Bruno Santos]

>You are running on Windows, so the paths should have "\" rather than "/" 
>in them.  However, in many cases this isn't essential - and indeed for 
>some Unix programs ported to Windows using "/" is sometimes best!
>
> my_blast_db = (r'e:/nt.00')
>
>I'm not sure if that is correct, but its difficult to tell without 
>seeing your setup.
It's ok to use the "/" because it seems that the python interpreter converts
it to the symbol used by the OS. 

> my_blast_file =
> r'C:/FASTASeq/Results/well9/assembled_file_well9_V6_DIST.fna'
> my_blast_exe = r'C:/BLAST/bin/'
>
>That is wrong, try something like:
>my_blast_exe = r'C:\BLAST\bin\blastall.exe'

You were right about that. It's ok now

> As I have download the files from ncbi I have a lot of files in the
database
> directory theres is any way of perform a search against all of them?

>I'm not sure what exactly you are asking.  BLAST can make databases from 
>FASTA files, so you might want to build a database from all your FASTA 
>files... check the documentation for the BLAST formatdb program.
I have downloaded the pre compiled files which mean I have five different
files like (nt.00.nhr, nt.01.nhr, nt.02.nhr...) and also the same files with
all the others extensions. But I have found I can use them all at the same
time by passing it to command line between "". So now I have my_blast_db =
(r'\"e:/nt.00 e:/nt.01 e:/nt.02 e:/nt.03 e:/nt.04 e:/nt.05 \"'). 

But now I'm mailing you with another doubt it is possible to pass the
result_handle to blast_results line by line or something like that because
I'm having a memory error in the step described below

result_handle, error_info = NCBIStandalone.blastall(my_blast_exe,
"blastn",my_blast_db, my_blast_file)
blast_results = result_handle.read() #Catch the results 

Maybe if I pass one line at a time and write ir immediately to the xml file
it will work. 

Thanks once more,
Bruno Santos