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1 #!/usr/bin/env python
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2 """
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3 Python script, served as the entry of open reading frame searching tool
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4 Separated the API with actual functionality (for Galaxy and future Web API)
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5
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6 Use -v or --version to get the version, -h or --help for help.
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7
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8 Author Nedias Sept 2016
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9
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10 """
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11 import sys
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12 from optparse import OptionParser
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13 import orf_tool
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14
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15 # Usage message
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16 usage = """Use as follows:
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17 $ python entry.py -i input_seq_file -l length_of_designated_match
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18 """
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19
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20 # User OptionParser to separate all optional arguments of the commandline
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21 parser = OptionParser(usage=usage)
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22 parser.add_option('-i', '--input', dest='input',
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23 default=None, help='Input sequences filename',
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24 metavar="FILE")
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25 parser.add_option("-l", "--length", dest="length",
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26 default=100,
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27 help="Set the length of designated match, length is the percentage of the longest match")
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28 parser.add_option("-f", "--format", dest="format",
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29 default="fasta",
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30 help="Set the format of input file")
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31 parser.add_option("-v", "--version", dest="version",
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32 default=False, action="store_true",
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33 help="Show version and quit")
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34 parser.add_option("-a", "--outputall", dest="outputa",
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35 default=None,
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36 help="Output of all matches",
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37 metavar="FILE")
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38 parser.add_option("-d", "--outputdest", dest="outputd",
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39 default=None,
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40 help="Output of designated matches",
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41 metavar="FILE")
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42
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43 options, args = parser.parse_args()
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44
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45 # Show version data (TODO:consider move to orf_tool.py)
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46 if options.version:
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47 print("v0.1.0")
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48 sys.exit(0)
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49
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50 # Call actual function
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51 else:
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52 orf_tool.exec_tool(options)
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53
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54
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