Mercurial > repos > rmarenco > hubarchivecreator
annotate Psl.py @ 26:df42241d3731 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
author | yating-l |
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date | Mon, 03 Jul 2017 17:30:20 -0400 |
parents | 2677f1899aa8 |
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rev | line source |
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3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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changeset
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1 import logging |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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2 import os |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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3 import tempfile |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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4 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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5 # Internal dependencies |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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6 from Datatype import Datatype |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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7 from util import subtools |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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8 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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9 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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10 class Psl(Datatype): |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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11 def __init__(self, input_psl_path, data_psl): |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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12 super(Psl, self).__init__() |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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13 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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14 self.track = None |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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15 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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16 self.input_psl_path = input_psl_path |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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17 self.name_psl = data_psl["name"] |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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18 self.priority = data_psl["order_index"] |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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19 self.track_color = data_psl["track_color"] |
17
c02720d1afee
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents:
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20 # TODO: Think about how to avoid repetition of the group_name everywhere |
c02720d1afee
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents:
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21 self.group_name = data_psl["group_name"] |
26
df42241d3731
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents:
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22 self.database = data_psl["database"] |
23
2677f1899aa8
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents:
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23 if data_psl["long_label"]: |
2677f1899aa8
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents:
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24 self.long_label = data_psl["long_label"] |
2677f1899aa8
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents:
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25 else: |
2677f1899aa8
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
parents:
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26 self.long_label = self.name_psl |
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3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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changeset
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27 # Temporary files |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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28 unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl') |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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29 sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl') |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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30 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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31 # Get the bed12+12 with pslToBigPsl |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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32 subtools.pslToBigPsl(input_psl_path, unsorted_bed_formatted_psl_file.name) |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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33 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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34 # Sort the formatted psl into sorted_bed_formatted_psl_file |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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35 subtools.sort(unsorted_bed_formatted_psl_file.name, sorted_bed_formatted_psl_file.name) |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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36 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
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37 # Get the binary indexed bigPsl with bedToBigBed |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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38 trackName = "".join((self.name_psl, ".bb")) |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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39 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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40 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as') |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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41 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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42 my_big_psl_file_path = os.path.join(self.myTrackFolderPath, trackName) |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
changeset
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43 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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44 logging.debug("Hello") |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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changeset
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45 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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46 with open(my_big_psl_file_path, 'w') as big_psl_file: |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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47 subtools.bedToBigBed(sorted_bed_formatted_psl_file.name, |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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48 self.chromSizesFile.name, |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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49 big_psl_file.name, |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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50 autoSql=auto_sql_option, |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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51 typeOption='bed12+12', |
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df42241d3731
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
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52 tab=True, |
df42241d3731
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
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53 extraIndex='name') |
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3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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54 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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55 # Create the Track Object |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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56 self.createTrack(file_path=trackName, |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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57 track_name=trackName, |
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2677f1899aa8
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
yating-l
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58 long_label=self.long_label, |
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3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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59 track_type='bigPsl', visibility='dense', |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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changeset
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60 priority=self.priority, |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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61 track_file=my_big_psl_file_path, |
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c02720d1afee
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
rmarenco
parents:
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62 track_color=self.track_color, |
26
df42241d3731
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents:
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63 group_name=self.group_name, |
df42241d3731
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
yating-l
parents:
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64 database=self.database) |
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3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
diff
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65 |
3233451a3bd6
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents:
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66 print("- BigPsl %s created" % self.name_psl) |