Mercurial > repos > iuc > resize_coordinate_window

annotate resize_coordinate_window.py @ 4:4eb3cc1f8466 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
author iuc
date Wed, 11 Dec 2019 18:06:42 -0500
parents 9ba78e8985dc
children
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4eb3cc1f8466 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
iuc
parents: 3
diff changeset
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4eb3cc1f8466 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
iuc
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08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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3 import argparse
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iuc
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4 import fileinput
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iuc
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5 import sys
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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6
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iuc
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7 # Maximum value of a signed 32 bit integer (2**31 - 1).
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8 MAX_CHROM_LEN = 2147483647
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11 def stop_err(msg):
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4eb3cc1f8466 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
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12 sys.exit(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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15 parser = argparse.ArgumentParser()
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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16 parser.add_argument('--input', dest='input', help="Input dataset")
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17 parser.add_argument('--start_coordinate', dest='start_coordinate', type=int, help='Chromosome start coordinate, either 0 or 1.')
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iuc
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18 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'
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19 parser.add_argument('--add_to_end', dest='add_to_end', type=int, help='Distance to add to end.')
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iuc
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20 parser.add_argument('--extend_existing', dest='extend_existing', help='Extend existing start/end instead of from computed midpoint.')
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iuc
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21 parser.add_argument('--chrom_len_file', dest='chrom_len_file', help="File names of .len files for chromosome lengths")
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22 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'
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23 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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24 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'
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26 extend_existing = args.extend_existing == 'existing'
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iuc
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27 out = open(args.output, 'w')
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iuc
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29 chrom_start = int(args.start_coordinate)
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iuc
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30 chrom_lens = dict()
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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31 # 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
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32 len_file_missing = False
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iuc
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33 len_file_error = None
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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34 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
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35 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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36 for line in len_file:
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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37 fields = 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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38 chrom_lens[fields[0]] = int(fields[1])
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39 except Exception as e:
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40 len_file_error = str(e)
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41
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42 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
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43 for line in fhi:
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44 if line.startswith('#'):
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45 # Skip comments.
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46 continue
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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47 items = line.split('\t')
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48 if len(items) != 9:
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49 # Skip invalid gff data.
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50 continue
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51 chrom = items[0]
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52 start = int(items[3])
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53 end = int(items[4])
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54 if extend_existing:
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55 new_start = start - args.subtract_from_start
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56 new_end = end + args.add_to_end
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57 else:
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58 midpoint = (start + end) // 2
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59 new_start = midpoint - args.subtract_from_start
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60 new_end = midpoint + args.add_to_end
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61 # Check start boundary.
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62 if new_start < chrom_start:
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63 if args.region_boundaries == 'discard':
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64 continue
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65 elif args.region_boundaries == 'limit':
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66 new_start = chrom_start
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67 elif args.region_boundaries == 'error':
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68 out.close()
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69 stop_err('Requested expansion places region beyond chromosome start boundary of %d.' % chrom_start)
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70 # Check end boundary.
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71 chrom_len = chrom_lens.get(chrom, None)
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72 if chrom_len is None:
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73 len_file_missing = True
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74 chrom_len = MAX_CHROM_LEN
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75 if new_end > chrom_len:
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76 if args.region_boundaries == 'discard':
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77 continue
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78 elif args.region_boundaries == 'limit':
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79 new_end = chrom_len
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80 elif args.region_boundaries == 'error':
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81 out.close()
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82 stop_err('Requested expansion places region beyond chromosome end boundary of %d.' % chrom_len)
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83 new_line = '\t'.join([chrom, items[1], items[2], str(new_start), str(new_end), items[5], items[6], items[7], items[8]])
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84 out.write(new_line)
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85 out.close()
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
86
1
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_error is not None:
4
4eb3cc1f8466 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
iuc
parents: 3
diff changeset
88 print("All chrom lengths set to %d, error in chrom len file: %s" % (MAX_CHROM_LEN, len_file_error))
1
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
iuc
parents: 0
diff changeset
89 if len_file_missing:
4
4eb3cc1f8466 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
iuc
parents: 3
diff changeset
90 print("All chrom lengths set to %d, chrom len files are not installed." % MAX_CHROM_LEN)