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annotate cytoBand.py @ 55:ba9997c847dc draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b2894a39921adaa6a93b12523820b61a78e11f20-dirty
author yating-l
date Wed, 17 May 2017 13:16:57 -0400
parents 4a58094b051e
children b39dd0b5a166
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4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
yating-l
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1 #!/usr/bin/python
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2
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3 import os
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4 import tempfile
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5
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6 from Datatype import Datatype
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7 from Track import Track
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
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8 from TrackDb import TrackDb
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9 from util import subtools
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10
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12 class cytoBand( Datatype ):
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13 def __init__(self, input_bed_cytoBand_false_path, data_bed_cytoBand):
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15 super(cytoBand, self).__init__()
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17 self.input_bed_cytoBand_false_path = input_bed_cytoBand_false_path
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18 self.name_bed_cytoBand = data_bed_cytoBand["name"]
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19 self.priority = data_bed_cytoBand["order_index"]
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20 self.track_color = data_bed_cytoBand["track_color"]
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21 # TODO: Think about how to avoid repetition of the group_name everywhere
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22 self.group_name = data_bed_cytoBand["group_name"]
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23 if data_bed_cytoBand["long_label"]:
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24 self.long_label = data_bed_cytoBand["long_label"]
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25 else:
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26 self.long_label = self.name_bed_cytoBand
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27 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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28
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29 # Sort processing
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30 subtools.sort(self.input_bed_cytoBand_false_path, sortedBedFile.name)
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32 # bedToBigBed processing
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33 # TODO: Change the name of the bb, to tool + genome + .bb
4a58094b051e planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 754b3f960221a68b90f9cddd98a1c3dd324d4d4e-dirty
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34 trackName = "".join( ( self.name_bed_cytoBand, '.bb' ) )
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35 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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36
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37 auto_sql_option = os.path.join(self.tool_directory, 'cytoBandIdeo.as')
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38
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39 with open(myBigBedFilePath, 'w') as bigBedFile:
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40 subtools.bedToBigBed(sortedBedFile.name,
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41 self.chromSizesFile.name,
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42 bigBedFile.name,
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43 typeOption='bed4',
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44 autoSql=auto_sql_option)
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45
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46 # Create the Track Object
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47 self.createTrack(file_path=trackName,
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48 track_name='cytoBandIdeo',
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49 long_label=self.long_label,
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50 track_type='bigBed',
55
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51 visibility='dense',
54
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52 priority=self.priority,
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53 track_file=myBigBedFilePath,
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54 track_color=self.track_color,
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55 group_name=self.group_name)
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56
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57 # dataURL = "tracks/%s" % trackName
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58 #
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59 # trackDb = TrackDb(
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60 # trackName=trackName,
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61 # longLabel=self.name_bed_simple_repeats,
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62 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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63 # trackDataURL=dataURL,
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64 # trackType='bigBed 4 +',
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65 # visibility='dense',
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66 # priority=self.priority,
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67 # )
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68 #
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69 # self.track = Track(
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70 # trackFile=myBigBedFilePath,
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71 # trackDb=trackDb,
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72 # )
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73
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74 print("- Bed splice junctions %s created" % self.name_bed_cytoBand)
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75 #print("- %s created in %s" % (trackName, myBigBedFilePath))