Mercurial > repos > rmarenco > hubarchivecreator
diff Bed.py @ 10:acc233161f50 draft
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 |
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--- a/Bed.py Wed Jul 20 12:29:08 2016 -0400 +++ b/Bed.py Thu Jul 21 05:58:51 2016 -0400 @@ -11,19 +11,14 @@ class Bed( Datatype ): - def __init__( self, inputBedGeneric, data_bed_generic, - inputFastaFile, extra_files_path, tool_directory ): - super(Bed, self).__init__( - inputFastaFile, extra_files_path, tool_directory - ) + def __init__( self, inputBedGeneric, data_bed_generic): + super(Bed, self).__init__() self.track = None self.inputBedGeneric = inputBedGeneric self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") - self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes") - self.twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0) self.data_bed_generic = data_bed_generic self.name_bed_generic = self.data_bed_generic["name"] @@ -32,15 +27,6 @@ # Sort processing subtools.sort(self.inputBedGeneric, self.sortedBedFile.name) - # Generate the chrom.sizes - # TODO: Isolate in a function - # We first get the twoBit Infos - subtools.twoBitInfo(self.twoBitFile.name, self.twoBitInfoFile.name) - - # Then we get the output to inject into the sort - # TODO: Check if no errors - subtools.sortChromSizes(self.twoBitInfoFile.name, self.chromSizesFile.name) - # bedToBigBed processing # TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb trackName = "".join( ( self.name_bed_generic, ".bb") )