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annotate BigBed.py @ 59:f311e21ef362 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 72268f816f10341dbe3f6b33f8d9170d859c9697-dirty
author yating-l
date Fri, 30 Jun 2017 15:50:57 -0400
parents b39dd0b5a166
children
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1 #!/usr/bin/python
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3 import os
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4 import shutil
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5 from subprocess import Popen, PIPE
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6 import re
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8 # Internal dependencies
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9 from Datatype import Datatype
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11 class BigBed(Datatype):
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12 """ Configurations for creating the bigBed evidence track """
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14 def __init__(self, input_bigbed_path, data_bigbed):
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15 super(BigBed, self).__init__()
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17 self.track = None
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19 self.input_bigbed_path = input_bigbed_path
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20 self.name_bigbed = data_bigbed["name"]
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21 self.priority = data_bigbed["order_index"]
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22 self.track_color = data_bigbed["track_color"]
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23 self.group_name = data_bigbed["group_name"]
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24 self.database = data_bigbed["database"]
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26 track_name = "".join((self.name_bigbed, ".bigbed"))
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27 if data_bigbed["long_label"]:
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28 self.long_label = data_bigbed["long_label"]
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29 else:
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30 self.long_label = self.name_bigbed
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32 bigbed_file_path = os.path.join(self.myTrackFolderPath, track_name)
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34 track_type = self.determine_track_type(input_bigbed_path)
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36 shutil.copy(self.input_bigbed_path, bigbed_file_path)
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38 # Create the Track Object
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39 self.createTrack(file_path=track_name,
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40 track_name=track_name,
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41 long_label=self.long_label,
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42 track_type=track_type,
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43 visibility='hide',
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44 priority=self.priority,
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45 track_file=bigbed_file_path,
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46 track_color=self.track_color,
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47 group_name=self.group_name,
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48 database=self.database)
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50 print "- BigBed %s created" % self.name_bigbed
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53 def determine_track_type(self, bb_file):
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54 """
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55 Determine the number of standard and extra fields using bigBedSummary
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57 Implementation of reading from stdout is based on a Stackoverflow post:
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58 http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate
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60 :param bb_file: path to a bigBed file
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62 :returns: the bigBed track type
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63 """
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65 cmd_ph = Popen(["bigBedSummary", "-fields", bb_file, "stdout"],
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66 stdout=PIPE, bufsize=1)
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68 pattern = r"(\d+) bed definition fields, (\d+) total fields"
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70 with cmd_ph.stdout:
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71 for line in iter(cmd_ph.stdout.readline, b''):
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72 match = re.match(pattern, line)
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74 if match:
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75 extra_mark = "." if match.group(1) == match.group(2) else "+"
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76 bed_type = "bigBed %s %s" % (match.group(1), extra_mark)
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77 break
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79 cmd_ph.wait()
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81 return bed_type