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annotate Gff3.py @ 11:d05236b15f81 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
author rmarenco
date Wed, 27 Jul 2016 10:10:49 -0400
parents acc233161f50
children 25809f699cb3
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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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6 # Internal dependencies
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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 Gff3( Datatype ):
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14 def __init__(self, input_Gff3_false_path, data_gff3):
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15 super( Gff3, self ).__init__()
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17 self.track = None
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19 self.input_Gff3_false_path = input_Gff3_false_path
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20 self.name_gff3 = data_gff3["name"]
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21 self.priority = data_gff3["order_index"]
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23 # TODO: See if we need these temporary files as part of the generated files
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24 genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
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25 unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
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26 sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
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28 # TODO: Refactor into another Class to manage the twoBitInfo and ChromSizes (same process as in Gtf.py)
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30 # gff3ToGenePred processing
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31 subtools.gff3ToGenePred(self.input_Gff3_false_path, genePredFile.name)
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33 # TODO: From there, refactor because common use with Gtf.py
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34 # genePredToBed processing
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35 subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)
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37 # Sort processing
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38 subtools.sort(unsortedBedFile.name, sortedBedFile.name)
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40 # TODO: Check if no errors
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42 # bedToBigBed processing
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43 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
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44 trackName = "".join( (self.name_gff3, ".bb" ) )
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45 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
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46 with open(myBigBedFilePath, 'w') as bigBedFile:
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47 subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
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49 # Create the Track Object
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50 self.createTrack(file_path=trackName,
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51 track_name=trackName,
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52 long_label=self.name_gff3, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
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53 track_file=myBigBedFilePath)
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54
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55 # dataURL = "tracks/%s" % trackName
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56 #
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57 # trackDb = TrackDb(
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58 # trackName=trackName,
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59 # longLabel=self.name_gff3,
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60 # shortLabel=self.getShortName( self.name_gff3 ),
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61 # trackDataURL=dataURL,
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62 # trackType='bigBed 12 +',
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63 # visibility='dense',
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64 # priority=self.priority,
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65 # )
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66 #
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67 # self.track = Track(
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68 # trackFile=myBigBedFilePath,
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69 # trackDb=trackDb,
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70 # )
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71
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72 print("- Gff3 %s created" % self.name_gff3)
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73 #print("- %s created in %s" % (trackName, myBigBedFilePath))