annotate interproscan5/fake_ips.py @ 9:1d6b3be059c8 draft default tip

Name change. Removed redundant tool def.
author mkh
date Mon, 08 Feb 2016 12:10:24 -0500
parents 74cf3f49f10c
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1 """
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2 """
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4 __author__ = 'mkh'
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6 if __name__ == '__main__':
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7 import argparse
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8 import os
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9 from shutil import copyfile
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10 import sys
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12 parser = argparse.ArgumentParser(description='Fake IPS.')
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14 parser.add_argument('-dp', action='store_true')
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15 parser.add_argument('--input')
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16 parser.add_argument('--seqtype', default='p')
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17 parser.add_argument('-f', dest='formats', default='tsv')
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18 parser.add_argument('--applications')
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19 parser.add_argument('--tempdir')
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20 parser.add_argument('--pathways', action='store_true')
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21 parser.add_argument('--goterms', action='store_true')
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22 parser.add_argument('--iprlookup', action='store_true')
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23 parser.add_argument('--mode')
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24 parser.add_argument('--clusterrunid')
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25 parser.add_argument('--output-file-base', dest='output_file_base')
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26 parser.add_argument('-o', dest='output_file', default="/tmp/junk")
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27
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28 args = parser.parse_args()
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29 formats = args.formats.split(',')
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30 src_data_dir = os.path.dirname(__file__) + '/data-' + args.seqtype
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32 for ext in formats:
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33 if ext in ['html', 'svg']:
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34 ext += '.tar.gz'
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35 copyfile(src_data_dir + '/' + '__base__' + '.' + ext, args.output_file_base + '.' + ext)