Mercurial > repos > iuc > resize_coordinate_window

annotate resize_coordinate_window.py @ 0:08b6255afde7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
author iuc
date Tue, 19 Jan 2016 09:34:56 -0500
parents
children 0164d2edba9f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
1 import argparse
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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2 import sys
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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3
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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4
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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5 def stop_err( msg ):
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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6 sys.stderr.write( msg )
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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7 sys.exit(1)
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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8
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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9 parser = argparse.ArgumentParser()
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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10 parser.add_argument('--input', dest='input', help="Input dataset")
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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11 parser.add_argument('--subtract_from_start', dest='subtract_from_start', type=int, help='Distance to subtract from start.')
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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12 parser.add_argument('--add_to_end', dest='add_to_end', type=int, help='Distance to add to end.')
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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13 parser.add_argument('--extend_existing', dest='extend_existing', help='Extend existing start/end rather or from computed midpoint.')
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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14 parser.add_argument('--output', dest='output', help="Output dataset")
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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15 args = parser.parse_args()
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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16
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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17 extend_existing = args.extend_existing == 'existing'
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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18 out = open(args.output, 'wb')
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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19
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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20 for line in open(args.input):
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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21 if line.startswith('#'):
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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22 continue
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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23 items = line.split('\t')
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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24 if len(items) != 9:
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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25 continue
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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26 start = int(items[3])
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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27 end = int(items[4])
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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28 if extend_existing:
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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29 start -= args.subtract_from_start
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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30 end += args.add_to_end
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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31 else:
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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32 midpoint = (start + end) // 2
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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33 start = midpoint - args.subtract_from_start
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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34 end = midpoint + args.add_to_end
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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35 if start < 1:
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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36 out.close()
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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37 stop_err('Requested expansion places region beyond chromosome bounds.')
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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38 new_line = '\t'.join([items[0], items[1], items[2], str(start), str(end), items[5], items[6], items[7], items[8]])
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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39 out.write(new_line)
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
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40 out.close()
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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