[Biopython-dev] 9/8 biopython Questions - BioStar

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// Biopython NCBIStandalone blastall gives different result than calling blastall directly from cmd
// September 7, 2010 at 7:36 PM

http://biostar.stackexchange.com/questions/2391/biopython-ncbistandalone-blastall-gives-different-result-than-calling-blastall-di
So, first I tested what results I should get from the blastall program using the command line, with e-value 0.001:

C:\Niek\Test\blast-2.2.17\bin\blastall -p blastp -d C:\Niek\Test\arabidopsis-smallproteins.fasta -i C:\Niek\Test\arabidopsis-HD.fasta -e 0.001 -F F -m 8 -o C:\Niek\Test\arab-HD-smallproteins-notfiltered.out


and

C:\Niek\Test\blast-2.2.17\bin\blastall -p blastp -d C:\Niek\Test\arabidopsis-smallproteins.fasta -i C:\Niek\Test\arabidopsis-HD.fasta -e 0.001 -m 8 -o C:\Niek\Test\arab-HD-smallproteins-filtered.out


After that I made a local blast program, which works fine but it only found 91 results with e-value equal or lower than 0.001, where the results from the blastall via cmd gave around 140~ something results. I first thought it missed some, but all the e-values are different.

from Bio.Blast import NCBIStandalone
from Bio.Blast import NCBIXML

my_blast_db = r"C:\Niek\Test\arabidopsis-smallproteins.fasta"
my_blast_file = r"C:\Niek\Test\arabidopsis-HD.fasta"
my_blast_exe =r"C:\Niek\blast-2.2.17\bin\blastall.exe"

result_handle, error_handle = NCBIStandalone.blastall(my_blast_exe, "blastp",
my_blast_db, my_blast_file)

blast_records = NCBIXML.parse(result_handle)

E_VALUE_THRESH = 0.001
x = 0
for blast_record in blast_records:
    blast_record = blast_records.next()
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
            if hsp.expect <= E_VALUE_THRESH:
                print "==========Alignment========"
                print "sequence:", alignment.title
                print "length:", alignment.length
                print "e value:", hsp.expect
                x += 1


I first thought that the local blast from biopython uses a different algorithm, but at 'my_blast_exe =r"C:\Niek\blast-2.2.17\bin\blastall.exe"' I specify the same program but it should be the same. Then I thought it had something to do with the filtering option but I checked both filtered and unfiltered and wasn't any of that.

If you know why the local blast from biopython NCBIStandalone gives a different result than doing it directly in the cmd, please let me know.

Thanks in advance,
Niek

edit: I checked, and it seems that the NCBIStandalone filters out 100% identities, which the blastall called by cmd does not. However this doesn't explain why the e-values are so different.


// Problem with blastp of biopython: returned non-zero exit status 1
// September 7, 2010 at 4:10 PM

http://biostar.stackexchange.com/questions/2388/problem-with-blastp-of-biopython-returned-non-zero-exit-status-1
I want to do a local BLAST using blastp from the Bio.Blast.Applications. However, when I run it I get a runtime error: returned non-zero exit status 1. According to the manual it is 
Exit Code Meaning: 1 Error in query sequence(s) or BLAST options. The query used is fasta format protein sequences.

The command line I used, with the BLAST options, was:
'>>> print blastp_cline 
C:\Program Files\NCBI\blast-2.2.24+\bin\blastp.exe -query "C:\Documents and Settings\newintern\Desktop\Microproteins_niek\arabidopsis-HD.fasta" -db C:\Documents and Settings\newintern\Desktop\Microproteins_niek\arabidopsis-smallproteins.fasta -out test.xml -evalue 0.001 -outfmt 5

Anyone know how to fix that error?

Thanks
Niek


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