annotate cofold.py @ 2:6fed0bc99753 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold commit 1527e05bcd748a2b3cef22e0e356697066a55635

#!/usr/bin/env python

import sys, os
import argparse
import shlex
import subprocess

parser = argparse.ArgumentParser()
parser.add_argument('-i', '--input', help='Input file name')
parser.add_argument('-o1','--output1', help='tabular output file')
parser.add_argument('-s', '--parameters', help='arguments')
args=parser.parse_args()

myinput = open(args.input)

parameters = args.parameters

# we assume that the param files are located next to the python dir
script_dir = os.path.dirname(os.path.realpath(__file__))
parameters = args.parameters.replace('-P ', '-P %s/' % script_dir)
p = subprocess.check_output(shlex.split('CoFold '+ parameters), stdin=myinput)

lines=p.split('\n')
# FASTA header
o=lines[0].replace('\t',' ')

for x in range(1, len(lines)):
    if x % 3 == 2:
        [seq,st]=lines[x].split(' ',1)
        st=st.strip().lstrip('(').rstrip(')')
        o+='\t' + seq + '\t' + st
    if x % 3 == 1:
        o+='\t'+lines[x]
    if x % 3 == 0:
        o+='\n'+lines[x].replace('\t',' ')
out=open(args.output1,'w')
out.write(o)
out.close()