Mercurial > repos > rnateam > cofold
comparison cofold.py @ 0:76d9140e8fa5 draft
Imported from capsule None
| author | bjoern-gruening |
|---|---|
| date | Fri, 13 Feb 2015 05:33:32 -0500 |
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| children |
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| -1:000000000000 | 0:76d9140e8fa5 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 import sys, os | |
| 4 import argparse | |
| 5 import shlex | |
| 6 import subprocess | |
| 7 | |
| 8 parser = argparse.ArgumentParser() | |
| 9 parser.add_argument('-i', '--input', help='Input file name') | |
| 10 parser.add_argument('-o1','--output1', help='tabular output file') | |
| 11 parser.add_argument('-s', '--parameters', help='arguments') | |
| 12 args=parser.parse_args() | |
| 13 | |
| 14 myinput = open(args.input) | |
| 15 | |
| 16 parameters = args.parameters | |
| 17 | |
| 18 # we assume that the param files are located next to the python dir | |
| 19 script_dir = os.path.dirname(os.path.realpath(__file__)) | |
| 20 parameters = args.parameters.replace('-P ', '-P %s/' % script_dir) | |
| 21 p = subprocess.check_output(shlex.split('CoFold '+ parameters), stdin=myinput) | |
| 22 | |
| 23 lines=p.split('\n') | |
| 24 # FASTA header | |
| 25 o=lines[0].replace('\t',' ') | |
| 26 | |
| 27 for x in range(1, len(lines)): | |
| 28 if x % 3 == 2: | |
| 29 [seq,st]=lines[x].split(' ',1) | |
| 30 st=st.strip().lstrip('(').rstrip(')') | |
| 31 o+='\t' + seq + '\t' + st | |
| 32 if x % 3 == 1: | |
| 33 o+='\t'+lines[x] | |
| 34 if x % 3 == 0: | |
| 35 o+='\n'+lines[x].replace('\t',' ') | |
| 36 out=open(args.output1,'w') | |
| 37 out.write(o) | |
| 38 out.close() | |
| 39 | |
| 40 | |
| 41 | |
| 42 | |
| 43 |