Mercurial > repos > iuc > resize_coordinate_window

annotate resize_coordinate_window.py @ 2:541f300f322d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
author iuc
date Mon, 14 Nov 2016 14:04:00 -0500
parents 0164d2edba9f
children 9ba78e8985dc
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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
1
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
parents: 0
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2 import fileinput
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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
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3 import sys
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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4
1
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
parents: 0
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5 # Maximum value of a signed 32 bit integer (2**31 - 1).
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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6 MAX_CHROM_LEN = 2147483647
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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
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0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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9 def stop_err(msg):
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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10 sys.stderr.write(msg)
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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
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11 sys.exit(1)
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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12
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 = argparse.ArgumentParser()
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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14 parser.add_argument('--input', dest='input', help="Input dataset")
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0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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15 parser.add_argument('--start_coordinate', dest='start_coordinate', type=int, help='Chromosome start coordinate, either 0 or 1.')
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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
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16 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
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17 parser.add_argument('--add_to_end', dest='add_to_end', type=int, help='Distance to add to end.')
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0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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18 parser.add_argument('--extend_existing', dest='extend_existing', help='Extend existing start/end instead of from computed midpoint.')
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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19 parser.add_argument('--chrom_len_file', dest='chrom_len_file', help="File names of .len files for chromosome lengths")
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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20 parser.add_argument('--region_boundaries', dest='region_boundaries', help="Option for handling region boundaries")
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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
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21 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
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22 args = parser.parse_args()
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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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
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24 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
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25 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'
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26
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0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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27 chrom_start = int(args.start_coordinate)
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
parents: 0
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28 chrom_lens = dict()
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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29 # Determine the length of each chromosome and add it to the chrom_lens dictionary.
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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30 len_file_missing = False
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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31 len_file_error = None
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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32 len_file = fileinput.FileInput(args.chrom_len_file)
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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33 try:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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34 for line in len_file:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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35 fields = line.split("\t")
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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36 chrom_lens[fields[0]] = int(fields[1])
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541f300f322d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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37 except Exception as e:
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0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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38 len_file_error = str(e)
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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39
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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40 with open(args.input) as fhi:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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41 for line in fhi:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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42 if line.startswith('#'):
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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43 # Skip comments.
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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44 continue
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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45 items = line.split('\t')
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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46 if len(items) != 9:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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47 # Skip invalid gff data.
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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48 continue
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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49 chrom = items[0]
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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50 start = int(items[3])
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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51 end = int(items[4])
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52 if extend_existing:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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53 new_start = start - args.subtract_from_start
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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54 new_end = end + args.add_to_end
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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55 else:
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56 midpoint = (start + end) // 2
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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57 new_start = midpoint - args.subtract_from_start
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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58 new_end = midpoint + args.add_to_end
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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59 # Check start boundary.
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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60 if new_start < chrom_start:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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61 if args.region_boundaries == 'discard':
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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62 continue
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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63 elif args.region_boundaries == 'limit':
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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64 new_start = chrom_start
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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65 elif args.region_boundaries == 'error':
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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66 out.close()
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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67 stop_err('Requested expansion places region beyond chromosome start boundary of %d.' % chrom_start)
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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68 # Check end boundary.
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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69 chrom_len = chrom_lens.get(chrom, None)
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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70 if chrom_len is None:
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71 len_file_missing = True
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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72 chrom_len = MAX_CHROM_LEN
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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73 if new_end > chrom_len:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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74 if args.region_boundaries == 'discard':
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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75 continue
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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76 elif args.region_boundaries == 'limit':
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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77 new_end = chrom_len
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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78 elif args.region_boundaries == 'error':
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
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79 out.close()
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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80 stop_err('Requested expansion places region beyond chromosome end boundary of %d.' % chrom_len)
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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81 new_line = '\t'.join([chrom, items[1], items[2], str(new_start), str(new_end), items[5], items[6], items[7], items[8]])
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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82 out.write(new_line)
0
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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83 out.close()
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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84
1
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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parents: 0
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85 if len_file_error is not None:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
parents: 0
diff changeset
86 print "All chrom lengths set to %d, error in chrom len file: %s" % (MAX_CHROM_LEN, len_file_error)
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
parents: 0
diff changeset
87 if len_file_missing:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
parents: 0
diff changeset
88 print "All chrom lengths set to %d, chrom len files are not installed." % MAX_CHROM_LEN