Error while running clustaw2 in biopython from script
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10.4 years ago
import re, sys, argparse, os, subprocess
from subprocess import call
from Bio import SeqIO
from Bio import AlignIO
from Bio.Seq import Seq
from Bio.Align.Applications import ClustalwCommandline

for key in store_seq:
    fileN=str(key)+".txt" #"1.txt"
    call(["touch",fileN])
    outFile=str(key)+".fasta" #"1.fasta"

    with open(fileN,'w') as f:
        f.write(">"+str(store_seq[key])+"\n") # print seq id
        f.write(str(chemo_seq[store_seq[key]] )+"\n")#print sequence
        f.write( ">"+str(brig_orth[store_seq[key]])+ "\n")
        f.write ( str(chemo_seq[brig_orth[store_seq[key]]]) +"\n")
        f.write( ">"+str(reman_orth[store_seq[key]]) +"\n" )
        f.write( str(chemo_seq[reman_orth[store_seq[key]]]) + "\n")
         #run clustalw2 for the file..--->    cline=ClustalwCommandline("clustalw2",infile=fileN,type="PROTEIN",output="FASTA",outfile=outFile,quiet)
    cline()

    #one key ends..

Error:cline=ClustalwCommandline("clustalw2",infile=fileN,type="PROTEIN",output="FASTA",outfile=outFile,quiet)
SyntaxError: non-keyword arg after keyword arg

However, when I run on python shell it runs smoothly. I have clustaw2 in my path. Instead of fileN and outFile, I give file name in double quotes.

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clustalw2 python2.7 biopython • 2.8k views
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This is a duplicate of http://seqanswers.com/forums/showthread.php?p=145887#post145887 - in future please don't ask the same question in multiple places without at least cross referencing.

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I apologize for it. I will refrain this in future.

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10.4 years ago
Andreas ★ 2.5k

Hi,

have a look at the error message again. You are using a non-keyword arg (quiet) after keywords arguments (key=value) which is incorrect Python Syntax. Just remove 'quiet' from ClustalwCommandline and it should work.

Andreas

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