Mercurial > repos > rmarenco > hubarchivecreator
comparison Bed.py @ 1:fb5e60d4d18a draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
| author | rmarenco |
|---|---|
| date | Wed, 13 Jul 2016 13:36:37 -0400 |
| parents | |
| children | acc233161f50 |
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| 0:0f3bc17e5ede | 1:fb5e60d4d18a |
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| 1 #!/usr/bin/python | |
| 2 | |
| 3 import os | |
| 4 import tempfile | |
| 5 | |
| 6 # Internal dependencies | |
| 7 from Datatype import Datatype | |
| 8 from Track import Track | |
| 9 from TrackDb import TrackDb | |
| 10 from util import subtools | |
| 11 | |
| 12 | |
| 13 class Bed( Datatype ): | |
| 14 def __init__( self, inputBedGeneric, data_bed_generic, | |
| 15 inputFastaFile, extra_files_path, tool_directory ): | |
| 16 super(Bed, self).__init__( | |
| 17 inputFastaFile, extra_files_path, tool_directory | |
| 18 ) | |
| 19 | |
| 20 self.track = None | |
| 21 | |
| 22 self.inputBedGeneric = inputBedGeneric | |
| 23 | |
| 24 self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") | |
| 25 self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes") | |
| 26 self.twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0) | |
| 27 | |
| 28 self.data_bed_generic = data_bed_generic | |
| 29 self.name_bed_generic = self.data_bed_generic["name"] | |
| 30 self.priority = self.data_bed_generic["order_index"] | |
| 31 | |
| 32 # Sort processing | |
| 33 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) | |
| 34 | |
| 35 # Generate the chrom.sizes | |
| 36 # TODO: Isolate in a function | |
| 37 # We first get the twoBit Infos | |
| 38 subtools.twoBitInfo(self.twoBitFile.name, self.twoBitInfoFile.name) | |
| 39 | |
| 40 # Then we get the output to inject into the sort | |
| 41 # TODO: Check if no errors | |
| 42 subtools.sortChromSizes(self.twoBitInfoFile.name, self.chromSizesFile.name) | |
| 43 | |
| 44 # bedToBigBed processing | |
| 45 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb | |
| 46 trackName = "".join( ( self.name_bed_generic, ".bb") ) | |
| 47 | |
| 48 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) | |
| 49 with open(myBigBedFilePath, 'w') as self.bigBedFile: | |
| 50 subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name) | |
| 51 | |
| 52 # Create the Track Object | |
| 53 dataURL = "tracks/%s" % trackName | |
| 54 | |
| 55 trackDb = TrackDb( | |
| 56 trackName=trackName, | |
| 57 longLabel=self.name_bed_generic, | |
| 58 shortLabel=self.getShortName(self.name_bed_generic), | |
| 59 trackDataURL=dataURL, | |
| 60 trackType='bigBed', | |
| 61 visibility='dense', | |
| 62 thickDrawItem='on', | |
| 63 priority=self.priority, | |
| 64 ) | |
| 65 | |
| 66 # Return the BigBed track | |
| 67 self.track = Track( | |
| 68 trackFile=myBigBedFilePath, | |
| 69 trackDb=trackDb, | |
| 70 ) | |
| 71 | |
| 72 print("- %s created in %s" % (trackName, myBigBedFilePath)) |