Error while running clustaw2 in biopython from script

Question

[Bioinformatics_NewComer]

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.

Editor using: emacs

[Peter]

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.

[Bioinformatics_NewComer]

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

Answer 1

[Andreas]

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