[BioPython] Running Blast locally

[Peter]

I didn't see this email - they arrived out of order at my computer. 
Please also read my longer reply...

Muthuraman, Manickam wrote:
> i have blast executable files in my home directory i.e
> /home/manickam/blast/blastall

Then use this:

my_blast_exe='/home/manickam/blast/blastall'

> i have my database files of nr,swissprot,pdb in /usr/junk/
> 
> the files which i can see under /usr/junk/        folder are 
> nr.00.phr    
>  nr.00.ppi  
> nr.01.phr     
> nr.01.ppi  nr.pal        
> pdbaa.00.msk
> 
> lot in there and there extenstions are *.phr , ppi ,pal,msk,psq

I think you should use one of these, but I haven't checked this:

my_blast_db='/usr/junk/nr'
my_blast_db='/usr/junk/swissprot'
my_blast_db='/usr/junk/pdb'

> i am not clear from the manual where do i need to provide the input sequences

The input fasta file can be anywhere - you just have to tell Blast where 
it is.  e.g.

my_blast_file='/home/manickam/Documents/m_cold.fasta')


 > and how to i store the out put after running the local blast.

If you run blast "by hand" at the command prompt, use the option -o 
outputfilename (that is a lower case letter o, not zero, not uppercase).

You can also using python to write the results to a file.

> below is the following code which i tried and it works but b_record is none.

See my other email

Peter