[BioPython] remote (PSI)blast and PSSM format

[alessandro.pandini at unimib.it]

Hi!

I have used biopython for some months... and it has made life much easier!
Thanks a lot!

I am trying to run remote blast and getting back PSSM matrices.
My goals are really simple:
-blast a sequence
-record only the pssm
-look at it in ascii format

So:

from Bio.Blast import NCBIWWW

bresults = NCBIWWW.blast('blastp', 
                         'nr',
                          seq, 
                          format_object = 'PSSM', 
                          format_type='Text')
b = bresults.read()
fout = open("pssm.dat",'w')
fout.write(b)
fout.close()

1. I had to comment the following in NCBIWWW.py:
794      #if results_params.has_key("FORMAT_OBJECT"):
795      #    del results_params["FORMAT_OBJECT"]
And the run did not fail...
Can I keep for save that if I got a result... it is a right one?
Which kind of failure is to be expected?

2. What I got back is:
PSSM:2
425A68313141592653592CF4248F000344FF50FFF8001000017D203FEFFF20800140007F800007C0027B9C005C4354F49931
0099A8068D034D1A69E9341A681A6114D253F541A1919000000000D3D550F481A1906868D068D0068D340044A6A932191A0D
34D3401A001A0D3085EC3A2B249CE1EBF02774797501030080610C333219902C8912010842048422C8C8C2041069DE8851B6
8212E5800E1948B058DAC0A0B635CD7B189C3D58B34F0890021A10C9CC9451100DA648852296C4421C44429DA192428C3731
F331893259082E4ECCFF2CD71AC164A042049488DAC20A6E2D910C410DEA66E050C2701758CC2A055284342812AEE4EB454C
60E49DADA2B4F6C2473D8443D2B0F969B112E37CD60D1587641C61909B3C3161D73DBC0AA1076E37BB7158DF71955ABBD17A
B42CC1140FA1BDD081E2E0725C8D8964AC10B54221C5E1933210D1475B2B364D056F6549A0419D0DB44DD869A811214A6D42
8A6C6D35976C4422948049D341370D3890089451DB13070806C6A20EA008A61BA6D2340E92209263155AAAB0A40C5861F082
B86D9E336000A1070DB74106F025C20E183C5255AEB1864AC946E432FDEB98F450F956AB69A8D5DA40F622A8693B7AB6D17D
C17DD565E68CD3BC678F04895294D4C261711DD7E69E11103B0188CEBC4FA6E5DEB3921488D61F952912310C6141284AD0DB
E30A8A38163349111332324D5C57CC070073C8F9861BF147D73140356CBA182AF77A7BC8F87B592B815047FC5DC914E14240
B3D0923C

I tried to find more on the checkpoint file format around NCBI and the web, but
I could not figure out anything. I am to lazy to look in the C code of ncbitools.
Which format is this? Is not supposed to be text format? How can I convert it?
Anything in biopython?

3. Once I got the PSSM can I use biopython to run a remote PSIblast? It looks
like PSSM parameter can not be set. Why? 

Thanks
Alex