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1 #!/usr/bin/env python
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2
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3 import sys, os
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4 import argparse
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5 import shlex
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6 import subprocess
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7
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8 parser = argparse.ArgumentParser()
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9 parser.add_argument('-i', '--input', help='Input file name')
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10 parser.add_argument('-o1','--output1', help='tabular output file')
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11 parser.add_argument('-s', '--parameters', help='arguments')
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12 args=parser.parse_args()
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13
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14 myinput = open(args.input)
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15
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16 parameters = args.parameters
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17
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18 # we assume that the param files are located next to the python dir
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19 script_dir = os.path.dirname(os.path.realpath(__file__))
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20 parameters = args.parameters.replace('-P ', '-P %s/' % script_dir)
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21 p = subprocess.check_output(shlex.split('CoFold '+ parameters), stdin=myinput)
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22
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23 lines=p.split('\n')
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24 # FASTA header
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25 o=lines[0].replace('\t',' ')
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26
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27 for x in range(1, len(lines)):
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28 if x % 3 == 2:
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29 [seq,st]=lines[x].split(' ',1)
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30 st=st.strip().lstrip('(').rstrip(')')
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31 o+='\t' + seq + '\t' + st
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32 if x % 3 == 1:
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33 o+='\t'+lines[x]
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34 if x % 3 == 0:
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35 o+='\n'+lines[x].replace('\t',' ')
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36 out=open(args.output1,'w')
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37 out.write(o)
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38 out.close()
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39
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