Question: NcbiblastpCommandline , not working properly in python but commands work on console
gravatar for New2programming
2.2 years ago by
New2programming0 wrote:

I'm trying to automate blast outputs from several files in a directory. Variables here are hardcoded but will be user defined later on. My infiles will be changed via a loop but i'm having issues running NcbiblastpCommandline on the files from within python.

from Bio.Blast.Applications import NcbiblastpCommandline
Filename2= 'Batch' + str(counter)
 from Bio.Blast.Applications import NcbiblastpCommandline
cline = NcbiblastpCommandline(query="minifasta.fasta", db="uniprot_database",outfmt=6, out=Filename2, evalue= E_Value_Thresh)
stdt,stdr= cline
NcbiblastpCommandline(cmd='blastp', query="minifasta.fasta", db="uniprot_database", outfmt=6, evalue= E_Value_Thresh)

I keep receiving an error saying ''NcbiblastpCommandline' object is not iterable.' and i'm being directed to the stdt,stdr line but without stdt,stdr another error saying the command isnt recogised comes up and error messages directing to stdout_str, stderr_str. I cant find up to date examples of NcbiblastpCommandline usage in python 3 to guide me.

ADD COMMENTlink modified 2.0 years ago by Biostar ♦♦ 20 • written 2.2 years ago by New2programming0
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