Mercurial > repos > yating-l > hubarchivecreator

annotate datatypes/Datatype.py @ 83:0bc486356e2a draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
author yating-l
date Mon, 30 Oct 2017 12:01:23 -0400
parents 2440ce10848b
children
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1 #!/usr/bin/python
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2 # -*- coding: utf8 -*-
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3
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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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7
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8 import os
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9 import tempfile
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10 import collections
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11 import util
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12 import logging
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13 import abc
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14 from abc import ABCMeta
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15 from TrackDb import TrackDb
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16 from datatypes.validators.DataValidation import DataValidation
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19 class Datatype(object):
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20 __metaclass__ = ABCMeta
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21
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22 twoBitFile = None
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23 chromSizesFile = None
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24 input_fasta_file = None
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25 extra_files_path = None
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26 tool_directory = None
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27
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28 mySpecieFolderPath = None
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29 myTrackFolderPath = None
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32 def __init__(self):
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33 not_init_message = "The {0} is not initialized." \
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34 "Did you use pre_init static method first?"
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35 if Datatype.input_fasta_file is None:
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36 raise TypeError(not_init_message.format('reference genome'))
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37 if Datatype.extra_files_path is None:
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38 raise TypeError(not_init_message.format('track Hub path'))
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39 if Datatype.tool_directory is None:
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40 raise TypeError(not_init_message.format('tool directory'))
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41 self.inputFile = None
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42 self.trackType = None
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43 self.dataType = None
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44 self.track = None
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45 self.trackSettings = dict()
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46 self.extraSettings = collections.OrderedDict()
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47
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48 @staticmethod
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49 def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
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50 extra_files_path, tool_directory, specie_folder, tracks_folder):
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51 Datatype.extra_files_path = extra_files_path
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52 Datatype.tool_directory = tool_directory
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53
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54 # TODO: All this should be in TrackHub and not in Datatype
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55 Datatype.mySpecieFolderPath = specie_folder
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56 Datatype.myTrackFolderPath = tracks_folder
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57
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58 Datatype.input_fasta_file = reference_genome
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59
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60 # 2bit file creation from input fasta
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61 Datatype.twoBitFile = two_bit_path
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62 Datatype.chromSizesFile = chrom_sizes_file
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64 def generateCustomTrack(self):
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65 self.validateData()
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66 self.initSettings()
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67 #Create the track file
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68 self.createTrack()
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69 # Create the TrackDb Object
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70 self.createTrackDb()
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71 logging.debug("- %s %s created", self.dataType, self.trackName)
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74 @abc.abstractmethod
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75 def validateData(self):
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76 """validate the input data with DataValidation"""
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77
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78 def initSettings(self):
66
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79 #Initialize required fields: trackName, longLabel, shortLable
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80 self.trackName = self.trackSettings["name"]
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81 if self.trackSettings["long_label"]:
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82 self.longLabel = self.trackSettings["long_label"]
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83 else:
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84 self.longLabel = self.trackName
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85 if not "short_label" in self.trackSettings:
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86 self.shortLabel = ""
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87 else:
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88 self.shortLabel = self.trackSettings["short_label"]
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89 self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName)
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90
66
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91
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92 @abc.abstractmethod
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93 def createTrack(self):
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94 """Create the final track file"""
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95
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96 def createTrackDb(self):
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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97 self.track = TrackDb(self.trackName, self.longLabel, self.shortLabel, self.trackDataURL, self.trackType, self.extraSettings)
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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98