Mercurial > repos > yating-l > hubarchivecreator

annotate datatypes/Datatype.py @ 72:2440ce10848b draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit a60f8496cccf4c5a07ba7d75876198eda997f07d
author yating-l
date Wed, 27 Sep 2017 15:34:20 -0400
parents 4ca7cbf2d9b8
children 0bc486356e2a
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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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17
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18
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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):
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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):
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97 self.track = TrackDb(self.trackName, self.longLabel, self.shortLabel, self.trackDataURL, self.trackType, self.extraSettings)
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98
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99
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100
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101
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102
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103
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104
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105 '''
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106 def __init__(self):
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107 not_init_message = "The {0} is not initialized." \
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108 "Did you use pre_init static method first?"
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109 if Datatype.input_fasta_file is None:
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110 raise TypeError(not_init_message.format('reference genome'))
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111 if Datatype.extra_files_path is None:
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112 raise TypeError(not_init_message.format('track Hub path'))
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113 if Datatype.tool_directory is None:
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114 raise TypeError(not_init_message.format('tool directory'))
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115 self.track = None
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116 self.extra_settings = collections.OrderedDict()
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117
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118
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119 @staticmethod
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120 def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
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121 extra_files_path, tool_directory, specie_folder, tracks_folder):
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122 Datatype.extra_files_path = extra_files_path
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123 Datatype.tool_directory = tool_directory
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124
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125 # TODO: All this should be in TrackHub and not in Datatype
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126 Datatype.mySpecieFolderPath = specie_folder
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127 Datatype.myTrackFolderPath = tracks_folder
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128
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129 Datatype.input_fasta_file = reference_genome
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130
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131 # 2bit file creation from input fasta
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132 Datatype.twoBitFile = two_bit_path
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133 Datatype.chromSizesFile = chrom_sizes_file
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134
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135 @staticmethod
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136 def get_largest_scaffold_name(self):
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137 # We can get the biggest scaffold here, with chromSizesFile
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138 with open(Datatype.chromSizesFile.name, 'r') as chrom_sizes:
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139 # TODO: Check if exists
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140 return chrom_sizes.readline().split()[0]
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141
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142
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143 def createTrack(self, trackName, longLabel, shortLabel, trackDataURL, trackType, extra_settings=None):
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144 self.track = TrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extra_settings)
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145
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146 def initRequiredSettings(self, trackSettings, trackDataURL = None, trackType = None):
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147
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148 #Initialize required fields: trackName, longLabel, shortLable
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149
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150 self.trackSettings = trackSettings
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151 self.trackName = self.trackSettings["name"]
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152 #self.priority = self.trackSettings["order_index"]
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153 #self.track_color = self.trackSettings["track_color"]
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154 # TODO: Think about how to avoid repetition of the group_name everywhere
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155 #self.group_name = self.trackSettings["group_name"]
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156 #self.database = self.trackSettings["database"]
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157 if self.trackSettings["long_label"]:
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158 self.longLabel = self.trackSettings["long_label"]
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159 else:
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160 self.longLabel = self.trackName
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161 if not "short_label" in self.trackSettings:
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162 self.shortLabel = ""
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163 else:
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164 self.shortLabel = self.trackSettings["short_label"]
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165 self.trackDataURL = trackDataURL
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166 self.trackType = trackType
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167
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168 def setExtLink(self, database, inputFile, seqType=None, useIframe=True, iframeHeight=None, iframeWidth=None):
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169 if "NCBI" in database:
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170 if not seqType:
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171 self.seqType = int(self.getSeqType(inputFile))
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172 else:
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173 self.seqType = seqType
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174 if self.seqType < 0:
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175 print self.seqType
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176 raise Exception("Sequence Type is not set for bigPsl. Stopping the application")
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177 if self.seqType == 2:
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178 self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$"
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179 elif self.seqType == 1:
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180 self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$"
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181 else:
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182 raise Exception("Sequence Type {0} is not valid for bigPsl. Stopping the application".format(self.seqType))
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183 elif "UniProt" in database:
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184 self.extra_settings["url"] = "http://www.uniprot.org/uniprot/$$"
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185 elif "FlyBase" in database:
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186 self.extra_settings["url"] = "http://flybase.org/reports/$$"
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187 else:
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188 self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
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189 self.extra_settings["urlLabel"] = database + " Details:"
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190 if useIframe:
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191 self.extra_settings["iframeUrl"] = self.extra_settings["url"]
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192 if not iframeHeight:
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193 iframeHeight = "600"
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194 if not iframeWidth:
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195 iframeWidth = "800"
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196 self.extra_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth)
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197
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198 def getSeqType(self, inputFile):
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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199 with open(inputFile, "r") as bigpsl:
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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200 sampleSeq = bigpsl.readline().split()
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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201 if len(sampleSeq) == 25:
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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202 return sampleSeq[-1]
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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203 else:
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204 return "-1"
4ca7cbf2d9b8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
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205 '''