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annotate BigWig.py @ 28:6aa28a85cc38 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5bbecd016ad3a784ad030cb82a09a3ac40dc6060
author yating-l
date Mon, 10 Jul 2017 17:08:38 -0400
parents df42241d3731
children
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rmarenco
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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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yating-l
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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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10 from Track import Track
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11 from TrackDb import TrackDb
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14 class BigWig( Datatype ):
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15 def __init__(self, input_bigwig_path, data_bigwig):
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16 super(BigWig, self).__init__()
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18 self.track = None
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20 self.input_bigwig_path = input_bigwig_path
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21 self.name_bigwig = data_bigwig["name"]
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22 self.priority = data_bigwig["order_index"]
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23 self.track_color = data_bigwig["track_color"]
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24 # TODO: Think about how to avoid repetition of the group_name everywhere
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25 self.group_name = data_bigwig["group_name"]
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26 self.database = data_bigwig["database"]
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27 if data_bigwig["long_label"]:
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28 self.long_label = data_bigwig["long_label"]
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29 else:
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30 self.long_label = self.name_bigwig
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31 #print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig )
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33 trackName = "".join( ( self.name_bigwig, ".bigwig" ) )
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35 myBigWigFilePath = os.path.join(self.myTrackFolderPath, trackName)
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36 shutil.copy(self.input_bigwig_path, myBigWigFilePath)
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38 # Create the Track Object
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39 self.createTrack(file_path=trackName,
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40 track_name=trackName,
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41 long_label=self.long_label,
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42 track_type=self.determine_track_type(myBigWigFilePath),
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43 visibility='full',
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44 priority=self.priority,
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45 track_file=myBigWigFilePath,
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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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49
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50 print("- BigWig %s created" % self.name_bigwig)
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51 #print("- %s created in %s" % (trackName, myBigWigFilePath))
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53 def determine_track_type(self, bw_file):
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54 """
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55 bigWig tracks must declare the expected signal range for the data
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yating-l
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56 (See https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html).
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57 This method determines the range of values for a bigWig file using
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yating-l
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58 the bigWigInfo program.
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60 Implementation of reading from stdout is based on a Stackoverflow post:
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61 http://stackoverflow.com/questions/2715847/python-read-streaming-input-from-subprocess-communicate
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63 :param bw_file: path to a bigWig file
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65 :returns: the bigWig track type
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66 """
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67 cmd_ph = Popen(["bigWigInfo", "-minMax", bw_file],
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68 stdout=PIPE, bufsize=1)
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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 bw_type = "bigWig %s" % line.rstrip()
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74 cmd_ph.wait()
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76 return bw_type