Mercurial > repos > devteam > ucsc_custom_track

annotate build_ucsc_custom_track.py @ 2:3d87079756e1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
author devteam
date Mon, 28 Feb 2022 20:06:04 +0000
parents 618e56c3109b
children
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0
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1 #!/usr/bin/env python
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2 """
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3 Build a UCSC genome browser custom track file
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4 """
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5
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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6 import sys
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7
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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8 FILE_TYPE_TO_TRACK_TYPE = {'bed': None, 'bedstrict': None, 'bed6': None, 'bed12': None, 'bedgraph': 'bedGraph', 'wig': 'wiggle_0'}
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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9 CHUNK_SIZE = 2**20 # 1 mb
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10
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11
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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12 def get_track_line_is_interval(file_type, name, description, color, visibility):
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13 if file_type in FILE_TYPE_TO_TRACK_TYPE:
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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14 track_type = FILE_TYPE_TO_TRACK_TYPE[file_type]
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15 is_interval = False
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16 else:
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17 track_type = None
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18 is_interval = True
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19 track_line = 'track '
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20 if track_type:
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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21 track_line += f"type={track_type} "
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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22 track_line += f'name="{name}" description="{description}" color={color} visibility={visibility}\n'
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23 return track_line, is_interval
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24
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25
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26 num_tracks = 0
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27 skipped_lines = 0
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28 first_invalid_line = 0
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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29 args = sys.argv[1:]
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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30 out_fname = args.pop(0)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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31 with open(out_fname, "w") as out:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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32 while args:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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33 # Suck in one dataset worth of arguments
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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34 in_fname = args.pop(0)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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35 file_type = args.pop(0)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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36 colspec = args.pop(0)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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37 name = args.pop(0)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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38 description = args.pop(0)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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39 color = args.pop(0).replace('-', ',')
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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40 visibility = args.pop(0)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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41 track_line, is_interval = get_track_line_is_interval(file_type, name, description, color, visibility)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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42 # Do the work
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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43 out.write(track_line)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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44 with open(in_fname) as in_file:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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45 if not is_interval:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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46 while True:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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47 chunk = in_file.read(CHUNK_SIZE)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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48 if chunk:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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49 out.write(chunk)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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50 else:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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51 break
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52 else:
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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53 # Assume type is interval (don't pass this script anything else!)
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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54 try:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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55 c, s, e, st = (int(x) - 1 for x in colspec.split(","))
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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56 except ValueError:
0
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57 try:
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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58 c, s, e = (int(x) - 1 for x in colspec.split(",")[:3])
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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59 st = -1 # strand column is absent
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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60 except Exception:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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61 sys.exit("Columns in interval file invalid for UCSC custom track.")
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62
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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63 i = 0
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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64 for i, line in enumerate(in_file):
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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65 line = line.rstrip('\r\n')
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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66 if line and not line.startswith('#'):
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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67 fields = line.split("\t")
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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68 if st > 0:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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69 # strand column is present
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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70 try:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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71 out.write(f"{fields[c]}\t{fields[s]}\t{fields[e]}\t{i}\t0\t{fields[st]}\n")
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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72 except Exception:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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73 skipped_lines += 1
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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74 if not first_invalid_line:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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75 first_invalid_line = i + 1
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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76 else:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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77 try:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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78 out.write(f"{fields[c]}\t{fields[s]}\t{fields[e]}\n")
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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79 except Exception:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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80 skipped_lines += 1
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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81 if not first_invalid_line:
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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82 first_invalid_line = i + 1
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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83 out.write("\n") # separating newline
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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84 num_tracks += 1
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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85
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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86 print(f"Generated a custom track containing {num_tracks} subtracks.")
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87 if skipped_lines:
2
3d87079756e1 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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88 print(f"Skipped {skipped_lines} invalid lines starting at #{first_invalid_line}")