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annotate Datatype.py @ 3:915aafec8726 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Thu, 14 Jul 2016 13:15:05 -0400
parents fb5e60d4d18a
children 816956489fe9
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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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14 def __init__( self, input_fasta_file, extra_files_path, tool_directory ):
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16 self.input_fasta_file = input_fasta_file
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17 self.extra_files_path = extra_files_path
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18 self.tool_directory = tool_directory
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21 # Construction of the arborescence
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22 # TODO: Change the hard-coded path with a input based one
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23 self.mySpecieFolderPath = os.path.join(extra_files_path, "myHub", "dbia3")
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25 # TODO: Refactor the name of the folder "tracks" into one variable, and should be inside TrackHub object
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26 self.myTrackFolderPath = os.path.join(self.mySpecieFolderPath, "tracks")
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28 # TODO: Redundant, should be refactored because they are all doing it...into hubArchiveCreator?
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29 # 2bit file creation from input fasta
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30 self.twoBitFile = subtools.faToTwoBit(self.input_fasta_file, self.mySpecieFolderPath)
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32 def getShortName( self, name_to_shortify ):
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33 # Slice to get from Long label the short label
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34 short_label_slice = slice(0, 15)
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36 return name_to_shortify[short_label_slice]