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1 # -*- coding: utf-8 -*-
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2 """
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3 Mugsy wrapper
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4
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5 For draft genomes a single multi-FASTA file containig all contigs should be provided.
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6 """
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7
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8 import optparse
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9 import os
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10 import shutil
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11 import subprocess
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12 import sys
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13 import tempfile
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14
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15 def __main__():
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16 """ main function """
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17 parser = optparse.OptionParser()
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18 parser.add_option('-r', dest='reference', help='reference FASTA file')
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19 parser.add_option('-c', dest='contigs', help='contigs FASTA file')
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20 parser.add_option('-p', dest='prefix', default='prefix', help='prefix ')
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21 parser.add_option('-l', dest='logfile', help='logfile')
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22 parser.add_option('--ml', dest='mugsylog', help='mugsylog file')
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23 parser.add_option('--maf', dest='maf', help='ouput MAF alignment file ')
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24 (options, args) = parser.parse_args()
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25 if len(args) > 0:
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26 parser.error('Wrong number of arguments')
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27
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28 logfile = options.logfile
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29 wd = tempfile.mkdtemp()
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30 try:
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31 command = "mugsy --directory %s --prefix %s --log %s %s %s" % (wd, options.prefix, options.mugsylog, options.reference, options.contigs)
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32 print 'Mugsy command to be executed:\n ' + command
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33
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34 log = open(logfile, 'w') if logfile else sys.stdout
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35 try:
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36 subprocess.check_call(command, stderr=log, shell=True) # need to redirect stderr because mugsy writes its logging info there
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37 finally:
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38 if log != sys.stdout:
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39 log.close()
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40 print 'Mugsy executed!'
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41
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42 shutil.move(os.path.join(wd, options.prefix + '.maf'), options.maf)
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43 finally:
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44 shutil.rmtree(wd)
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45
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46
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47 if __name__ == "__main__":
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48 __main__()
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