Mercurial > repos > rmarenco > hubarchivecreator
annotate BigBed.py @ 25:99dad5f9444c draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
| author | yating-l |
|---|---|
| date | Fri, 02 Jun 2017 17:36:24 -0400 |
| parents | fcc1021bd496 |
| children | df42241d3731 |
| rev | line source |
|---|---|
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24
fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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1 #!/usr/bin/python |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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2 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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3 import os |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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4 import shutil |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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5 from subprocess import Popen, PIPE |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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6 import re |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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7 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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8 # Internal dependencies |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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9 from Datatype import Datatype |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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10 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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11 class BigBed(Datatype): |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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12 """ Configurations for creating the bigBed evidence track """ |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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13 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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14 def __init__(self, input_bigbed_path, data_bigbed): |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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15 super(BigBed, self).__init__() |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
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16 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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17 self.track = None |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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18 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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19 self.input_bigbed_path = input_bigbed_path |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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20 self.name_bigbed = data_bigbed["name"] |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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21 self.priority = data_bigbed["order_index"] |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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22 self.track_color = data_bigbed["track_color"] |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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23 self.group_name = data_bigbed["group_name"] |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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24 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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25 track_name = "".join((self.name_bigbed, ".bigbed")) |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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26 if data_bigbed["long_label"]: |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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27 self.long_label = data_bigbed["long_label"] |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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28 else: |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
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29 self.long_label = self.name_bigbed |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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30 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
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31 bigbed_file_path = os.path.join(self.myTrackFolderPath, track_name) |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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32 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
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33 track_type = self.determine_track_type(input_bigbed_path) |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
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34 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
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35 shutil.copy(self.input_bigbed_path, bigbed_file_path) |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
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36 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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37 # Create the Track Object |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
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38 self.createTrack(file_path=track_name, |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
changeset
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39 track_name=track_name, |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
changeset
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40 long_label=self.long_label, |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
changeset
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41 track_type=track_type, |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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42 visibility='hide', |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
changeset
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43 priority=self.priority, |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
changeset
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44 track_file=bigbed_file_path, |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
changeset
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45 track_color=self.track_color, |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
diff
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46 group_name=self.group_name) |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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47 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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48 print "- BigBed %s created" % self.name_bigbed |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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49 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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50 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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51 def determine_track_type(self, bb_file): |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
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52 """ |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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53 Determine the number of standard and extra fields using bigBedSummary |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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54 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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55 Implementation of reading from stdout is based on a Stackoverflow post: |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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56 http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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57 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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58 :param bb_file: path to a bigBed file |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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59 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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60 :returns: the bigBed track type |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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61 """ |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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62 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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63 cmd_ph = Popen(["bigBedSummary", "-fields", bb_file, "stdout"], |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
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64 stdout=PIPE, bufsize=1) |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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65 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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66 pattern = r"(\d+) bed definition fields, (\d+) total fields" |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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67 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
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68 with cmd_ph.stdout: |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
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69 for line in iter(cmd_ph.stdout.readline, b''): |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
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70 match = re.match(pattern, line) |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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71 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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72 if match: |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
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73 extra_mark = "." if match.group(1) == match.group(2) else "+" |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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74 bed_type = "bigBed %s %s" % (match.group(1), extra_mark) |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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75 break |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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76 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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77 cmd_ph.wait() |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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78 |
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fcc1021bd496
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
yating-l
parents:
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79 return bed_type |