Code:
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
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
What is the cause for this?
How do I correct it?
Python 2.7
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