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annotate bigPsl.py @ 65:5a4206366b41 draft

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author yating-l
date Wed, 09 Aug 2017 16:40:21 -0400
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1 #!/usr/bin/python
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3 import os
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4 import tempfile
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5 import string
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7 from Datatype import Datatype
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8 from Track import Track
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9 from TrackDb import TrackDb
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10 from util import subtools
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13 class bigPsl( Datatype ):
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14 def __init__(self, input_bigpsl_false_path, data_bigpsl):
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16 super(bigPsl, self).__init__()
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18 self.input_bigpsl_false_path = input_bigpsl_false_path
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19 self.name_bigpsl = data_bigpsl["name"]
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20 self.priority = data_bigpsl["order_index"]
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21 self.track_color = data_bigpsl["track_color"]
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22 # TODO: Think about how to avoid repetition of the group_name everywhere
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23 self.group_name = data_bigpsl["group_name"]
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24 self.database = data_bigpsl["database"]
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25 if data_bigpsl["long_label"]:
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26 self.long_label = data_bigpsl["long_label"]
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27 else:
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28 self.long_label = self.name_bigpsl
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29 if data_bigpsl["search_index"]:
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30 self.search_index = data_bigpsl["search_index"]
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31 else:
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32 self.search_index = ""
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33 #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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35 # Sort processing
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36 #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name)
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38 # bedToBigBed processing
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39 # TODO: Change the name of the bb, to tool + genome + .bb
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40 trackName = "".join( ( self.name_bigpsl, '.bb' ) )
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42 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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44 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
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46 with open(myBigBedFilePath, 'w') as bigBedFile:
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47 subtools.bedToBigBed(self.input_bigpsl_false_path,
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48 self.chromSizesFile.name,
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49 bigBedFile.name,
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50 typeOption='bed12+12',
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51 tab='True',
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52 autoSql=auto_sql_option,
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53 extraIndex='name')
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55 self.createTrack(file_path=trackName,
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56 track_name=trackName,
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57 long_label=self.long_label, track_type='bigPsl', visibility='dense',
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58 priority=self.priority,
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59 track_file=myBigBedFilePath,
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60 track_color=self.track_color,
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61 group_name=self.group_name,
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62 database=self.database)
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64
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65 # dataURL = "tracks/%s" % trackName
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66 #
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67 # trackDb = TrackDb(
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68 # trackName=trackName,
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69 # longLabel=self.name_bed_simple_repeats,
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70 # shortLabel=self.getShortName( self.name_bed_simple_repeats ),
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71 # trackDataURL=dataURL,
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72 # trackType='bigBed 4 +',
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73 # visibility='dense',
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74 # priority=self.priority,
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75 # )
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76 #
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77 # self.track = Track(
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78 # trackFile=myBigBedFilePath,
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79 # trackDb=trackDb,
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80 # )
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82 print("- bigPsl %s created" % self.name_bigpsl)
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83 #print("- %s created in %s" % (trackName, myBigBedFilePath))