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comparison Bed.py @ 10:acc233161f50 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1b1063f90004764bcf504f4340738eca5c4b1f9d
author rmarenco
date Thu, 21 Jul 2016 05:58:51 -0400
parents fb5e60d4d18a
children d05236b15f81
comparison
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9:4f9847539a28 10:acc233161f50
9 from TrackDb import TrackDb 9 from TrackDb import TrackDb
10 from util import subtools 10 from util import subtools
11 11
12 12
13 class Bed( Datatype ): 13 class Bed( Datatype ):
14 def __init__( self, inputBedGeneric, data_bed_generic, 14 def __init__( self, inputBedGeneric, data_bed_generic):
15 inputFastaFile, extra_files_path, tool_directory ): 15 super(Bed, self).__init__()
16 super(Bed, self).__init__(
17 inputFastaFile, extra_files_path, tool_directory
18 )
19 16
20 self.track = None 17 self.track = None
21 18
22 self.inputBedGeneric = inputBedGeneric 19 self.inputBedGeneric = inputBedGeneric
23 20
24 self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") 21 self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
25 self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
26 self.twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
27 22
28 self.data_bed_generic = data_bed_generic 23 self.data_bed_generic = data_bed_generic
29 self.name_bed_generic = self.data_bed_generic["name"] 24 self.name_bed_generic = self.data_bed_generic["name"]
30 self.priority = self.data_bed_generic["order_index"] 25 self.priority = self.data_bed_generic["order_index"]
31 26
32 # Sort processing 27 # Sort processing
33 subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) 28 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 29
44 # bedToBigBed processing 30 # bedToBigBed processing
45 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb 31 # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
46 trackName = "".join( ( self.name_bed_generic, ".bb") ) 32 trackName = "".join( ( self.name_bed_generic, ".bb") )
47 33