[BioPython] Running local blast with aa

[Sebastian Bassi]

Hello,

I have a problem I think is a Python problem since when I trie to do it 
manually with the blast executable it works.
I´m running local BLAST (the standalone version under WinNT).
I did the test on the blast readme file and went OK. (the test was to 
blastn a ecoli sequence)
Then I tried to blastX an ecoli nucleitide sequence against the ecoli.aa 
database (I did formated the ecolia.aa with formatdb of course). The 
nucleotide sequence I used to test was:
 >test de prot
TATGAGCATACTTTGATGGCTTTGGAGGCTGGTTGTCATGTTATGTGTGAGAAGCCTCCTGCTATGACTCCTGAGCAGGC
TCGTGAGATGTGTGATACTGCTCGTAAGTTGGGTAAGGTTTTGGCTTATGATTTTCATCATCGTTTTGCTTTGGATACTC
AGCAGTTGCGTGAGCAGGTTACTAATGGTGTTTTGGGTGAGATTTATGTTACTACTGCTCGTGCT
This is a backtranslation from a part of an actual ecoli protein 
(AAC74397). (was backtranslated with python using table bacterial table, 
  11)
When I run this blast on the NCBI site, I get the original protein as a 
first hit (AAC74397). When I do it locally from the command line BLAST 
it also works fine.
But the problem is that when I do it locally using Python (I mean, the 
blastX against the ecoli.aa database) I get 0 hits. I´m using all 
standard/default values.
Here´s the output I get:

BLASTX 2.2.4 [Aug-26-2002]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= test de prot
          (225 letters)

Database: //server/bioinfo/blast/data/ecoli.aa
            4289 sequences; 1,358,990 total letters



  ***** No hits found ******

   Database: //server/bioinfo/blast/data/ecoli.aa
     Posted date:  Oct 25, 2002  8:30 AM
   Number of letters in database: 1,358,990
   Number of sequences in database:  4289

If you want to see my input file:

 >test de prot
TATGAGCATACTTTGATGGCTTTGGAGGCTGGTTGTCATGTTATGTGTGAGAAGCCTCCTGCTATGACTC
CTGAGCAGGCTCGTGAGATGTGTGATACTGCTCGTAAGTTGGGTAAGGTTTTGGCTTATGATTTTCATCA
TCGTTTTGCTTTGGATACTCAGCAGTTGCGTGAGCAGGTTACTAATGGTGTTTTGGGTGAGATTTATGTT
ACTACTGCTCGTGCT

And here is my little python program (BTW, it works fine for blastn, so 
I asume the program logic is OK).


from Bio.Blast import NCBIStandalone
import os
import string
import re

pathdb="//server/bioinfo/blast/data/ecoli.aa"
blastexe="//server/bioinfo/blast/blastall.exe"
pathin="D:\\projects\\bioinfo-adv\\set-cd-small\\"
filesentr="D:\\projects\\bioinfo-adv\\set-cd-small"
pathout="blastbatch\\outblast"

print "OK 1"
cont = 0

# mando todos los files de set-cd-complete a una lista

listaentrada=os.listdir(filesentr)
for x in listaentrada:
    cont = cont + 1
    blast_out, error_info = NCBIStandalone.blastall(blastexe, 'blastx', 
pathdb, pathin+x)
    salida=open(pathout+x+".txt","w")
    salida.writelines(blast_out)
    salida.close()
    print "Blast numero "+`cont`+" "+x
print "FIN"

print "OK 2 re ok"