[BioPython] Blast Error

[Omenkeukwu, Gregory]

> I get the following error when I run the BLAST code in the tutorial. I will appreciate any help I can get on this issue. Thanks
> 
> 
> 
> Warning (from warnings module):
>   File "C:\Python24\lib\site-packages\Bio\Blast\NCBIWWW.py", line 1070
>     warnings.warn("qblast works only with blastn and blastp for now.")
> UserWarning: qblast works only with blastn and blastp for now.
> 
> Traceback (most recent call last):
>   File "C:\Python24\biopython examples\blast_example.py", line 10, in -toplevel-
>     result_handle = NCBIWWW.qblast('blastn', 'nr', f_record)
>   File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIWWW.py", line 1092, in qblast
>     rid, rtoe = _parse_qblast_ref_page(handle)
>   File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIWWW.py", line 1177, in _parse_qblast_ref_page
>     return rid, int(rtoe)
> ValueError: invalid literal for int(): 1.0 400 We don't support 0.9
> 
> 
> 
> 
> 
> 
> just for reference, the code I am running is listed below
> 
> from Bio import Fasta
> 
> file_for_blast = open('m_cold.fasta', 'r')
> f_iterator = Fasta.Iterator(file_for_blast)
> 
> f_record = f_iterator.next()
> 
> 
> from Bio.Blast import NCBIWWW
> result_handle = NCBIWWW.qblast('blastn', 'nr', f_record)
> 
> 
> # save the results for later, in case we want to look at it
> save_file = open('my_blast.out', 'w')
> blast_results = result_handle.read()
> save_file.write(blast_results)
> save_file.close()
> 
> import cStringIO
> blast_out = cStringIO.StringIO(blast_results)
> 
> 
> blast_out = open('my_blast.out', 'r')
> 
> 
> from Bio.Blast import NCBIXML
> 
> b_parser = NCBIXML.BlastParser()
> b_record = b_parser.parse(blast_out)
> 
> E_VALUE_THRESH = 0.04
> 
> for alignment in b_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
>             print hsp.query[0:75] + '...'
>             print hsp.match[0:75] + '...'
>             print hsp.sbjct[0:75] + '...'
> 
> 
> Gregory Omenkeukwu
> Provider Information Management
> 



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