Mercurial > repos > yating-l > jbrowsearchivecreator

annotate datatypes/Datatype.py @ 47:1eb4adefd747 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 97a743ee6d228c8a0a5778ec3cb6f68a2e22c8e3
author yating-l
date Tue, 19 Jun 2018 17:39:12 -0400
parents 061da5d3a219
children
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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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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 from util import subtools
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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 tracks.HTMLFeatures import HTMLFeatures
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16 from tracks.CanvasFeatures import CanvasFeatures
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17 from tracks.BamFeatures import BamFeatures
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18 from tracks.BigwigFeatures import BigwigFeatures
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19 from datatypes.validators.DataValidation import DataValidation
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22 class Datatype(object):
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23 __metaclass__ = ABCMeta
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25 chromSizesFile = None
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26 input_fasta_file = None
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27 extra_files_path = None
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28 tool_directory = None
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30 mySpecieFolderPath = None
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31 myTrackFolderPath = None
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32 myBinaryFolderPath = None
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34 trackType = None
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36 def __init__(self):
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37 not_init_message = "The {0} is not initialized." \
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38 "Did you use pre_init static method first?"
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39 if Datatype.input_fasta_file is None:
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40 raise TypeError(not_init_message.format('reference genome'))
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41 if Datatype.extra_files_path is None:
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42 raise TypeError(not_init_message.format('track Hub path'))
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43 if Datatype.tool_directory is None:
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44 raise TypeError(not_init_message.format('tool directory'))
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45 self.inputFile = None
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46 self.trackType = None
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47 self.dataType = None
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48 self.trackFileType = None
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49 self.track = None
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50 self.trackSettings = dict()
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51 self.extraSettings = collections.OrderedDict()
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52
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54 @staticmethod
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55 def pre_init(reference_genome, chrom_sizes_file,
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56 extra_files_path, tool_directory, specie_folder, tracks_folder, binary_folder, track_type):
25
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57 Datatype.extra_files_path = extra_files_path
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58 Datatype.tool_directory = tool_directory
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59
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60 # TODO: All this should be in TrackHub and not in Datatype
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61 Datatype.mySpecieFolderPath = specie_folder
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62 Datatype.myTrackFolderPath = tracks_folder # temporary raw data files
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63 Datatype.myBinaryFolderPath = binary_folder
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64
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65 Datatype.input_fasta_file = reference_genome
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67 # 2bit file creation from input fasta
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68 #Datatype.twoBitFile = two_bit_path
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69 Datatype.chromSizesFile = chrom_sizes_file
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70 Datatype.trackType = track_type
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73 def generateCustomTrack(self):
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74 self.validateData()
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75 self.initSettings()
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76 #Create the track file
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77 self.createTrack()
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78 # Create the TrackDb Object
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79 self.createTrackDb()
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80 logging.debug("- %s %s created", self.dataType, self.trackName)
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81
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82
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83 @abc.abstractmethod
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84 def validateData(self):
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85 """validate the input data with DataValidation"""
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86
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87 def initSettings(self):
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88 #Initialize required fields: trackName, longLabel, shortLable
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89 self.trackName = self.trackSettings["name"]
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90 self.trackDataURL = os.path.join(self.myTrackFolderPath, self.trackName)
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91 if self.trackSettings["long_label"]:
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92 self.trackLabel = self.trackSettings["long_label"]
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93 else:
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94 self.trackLabel = self.trackName
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95 if "trackType" in self.trackSettings and self.trackSettings["trackType"]:
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96 self.trackType = self.trackSettings["trackType"]
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97 if self.trackSettings["group_name"]:
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98 self.extraSettings["category"] = self.trackSettings["group_name"]
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99 if "track_color" in self.trackSettings and self.trackSettings["track_color"]:
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100 self.extraSettings["color"] = self.trackSettings["track_color"]
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101 #store information of whether to generate name index for the track
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102 self.extraSettings["nameIndex"] = self.trackSettings["nameIndex"]
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103
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104
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105 @abc.abstractmethod
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106 def createTrack(self):
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107 """Create the final track file"""
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108
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109 def createTrackDb(self):
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110 if self.trackType == 'HTMLFeatures':
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111 self.track = HTMLFeatures(self.trackName, self.trackLabel, self.trackDataURL, self.trackType, self.dataType, self.extraSettings)
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112 elif self.trackType == "CanvasFeatures":
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113 self.track = CanvasFeatures(self.trackName, self.trackLabel, self.trackDataURL, self.trackType, self.dataType, self.extraSettings)
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114 elif self.trackType == "bam":
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115 self.track = BamFeatures(self.trackName, self.trackLabel, self.trackDataURL, self.trackType, self.dataType, self.extraSettings)
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116 elif self.trackType == "bigwig":
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117 self.track = BigwigFeatures(self.trackName, self.trackLabel, self.trackDataURL, self.trackType, self.dataType, self.extraSettings)
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118 else:
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119 logging.error("Cannot createTrackDb, because trackType is not defined or invalid! trackType = %s", self.trackType)
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120 self.track.createTrackDb()
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121
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122 #self.track = TrackDb(self.trackName, self.trackLabel, self.trackDataURL, self.trackType, self.dataType, self.extraSettings)
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123
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124