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annotate Datatype.py @ 6:816956489fe9 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 20817d2bd61639d88226c9cd0392cea420ded222
author rmarenco
date Tue, 19 Jul 2016 01:19:57 -0400
parents fb5e60d4d18a
children acc233161f50
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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4 """
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5 Super Class of the managed datatype
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6 """
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8 import os
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10 from util import subtools
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13 class Datatype(object):
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15 twoBitFile = None
816956489fe9 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 20817d2bd61639d88226c9cd0392cea420ded222
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17 def __init__( self, input_fasta_file, extra_files_path, tool_directory ):
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19 self.input_fasta_file = input_fasta_file
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20 self.extra_files_path = extra_files_path
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21 self.tool_directory = tool_directory
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23 self.twoBitFile = None
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25 # Construction of the arborescence
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26 # TODO: Change the hard-coded path with a input based one
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27 self.mySpecieFolderPath = os.path.join(extra_files_path, "myHub", "dbia3")
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29 # TODO: Refactor the name of the folder "tracks" into one variable, and should be inside TrackHub object
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30 self.myTrackFolderPath = os.path.join(self.mySpecieFolderPath, "tracks")
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32 # TODO: Redundant, should be refactored because they are all doing it...into hubArchiveCreator?
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33 # 2bit file creation from input fasta
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34 if not Datatype.twoBitFile:
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35 print "We create the self.twoBit in " + self.__class__.__name__
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36 Datatype.twoBitFile = subtools.faToTwoBit(self.input_fasta_file, self.mySpecieFolderPath)
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38 # TODO: Remove this by saying to all children classes to use "Datatype.twoBitFile" instead
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39 self.twoBitFile = Datatype.twoBitFile
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41 def getShortName( self, name_to_shortify ):
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42 # Slice to get from Long label the short label
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43 short_label_slice = slice(0, 15)
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45 return name_to_shortify[short_label_slice]