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
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 withou at least cross referencing.
I apologize for it. I will refrain this in future.