Mercurial > repos > yating-l > jbrowsearchivecreator

annotate TrackHub.py @ 7:5d5fdcb798da draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e
author yating-l
date Fri, 20 Apr 2018 13:51:23 -0400
parents 237707a6b74d
children 43a700afd457
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1 #!/usr/bin/env python
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3 import os
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4 import subprocess
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5 import shutil
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6 import zipfile
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7 import json
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8 import tempfile
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9 import logging
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10 from mako.lookup import TemplateLookup
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12 from datatypes.Datatype import Datatype
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13 from tracks.TrackStyles import TrackStyles
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14 from util import subtools
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15 from util import santitizer
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18 class TrackHub:
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19 def __init__(self, inputFastaFile, outputFile, extra_files_path, tool_directory, trackType):
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21 self.mySpecieFolderPath = None
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23 # Store intermediate files, will be removed if not in debug mode
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24 self.myTracksFolderPath = None
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26 # Store interval files and their tabix index
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27 self.myFinalTracksFolderPath = None
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29 # Store binary files: Bam, BigWig
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30 self.myBinaryFolderPath = None
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32 self.tool_directory = tool_directory
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33 self.trackType = trackType
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34 self.reference_genome = inputFastaFile
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35 self.genome_name = inputFastaFile.assembly_id
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36 self.extra_files_path = extra_files_path
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37 self.outputFile = outputFile
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38 self.chromSizesFile = None
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41 # Set all the missing variables of this class, and create physically the folders/files
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42 self.__createAssemblyHub__(extra_files_path=extra_files_path)
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43 # Init the Datatype
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44 Datatype.pre_init(self.reference_genome, self.chromSizesFile,
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45 self.extra_files_path, self.tool_directory,
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46 self.mySpecieFolderPath, self.myTracksFolderPath, self.myBinaryFolderPath, self.trackType)
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48 self._prepareRefseq()
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49 self.trackList = os.path.join(self.mySpecieFolderPath, "trackList.json")
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50 self._createTrackList()
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51 if Datatype.trackType == 'HTMLFeatures':
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52 self.myTrackStyle = TrackStyles(self.tool_directory, self.mySpecieFolderPath, self.trackList)
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53 self.logger = logging.getLogger(__name__)
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54
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55
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57 def addTrack(self, trackDbObject):
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58 if trackDbObject['dataType'].lower() == 'bam':
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59 subtools.add_track_json(self.trackList, trackDbObject['options'])
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60 elif trackDbObject['dataType'].lower() == 'bigwig':
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61 subtools.add_track_json(self.trackList, trackDbObject['options'])
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62 else:
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63 if trackDbObject['trackType'] == 'HTMLFeatures':
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64 self._customizeHTMLFeature(trackDbObject)
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65 subtools.flatfile_to_json(trackDbObject['trackDataURL'], trackDbObject['dataType'], trackDbObject['trackType'], trackDbObject['trackLabel'], self.mySpecieFolderPath, trackDbObject['options'])
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66 # Use Tabix index tracks by default for CanvasFeatures
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67 # TODO: add support for HTMLFeatures
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68 else:
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69 subtools.generate_tabix_indexed_track(trackDbObject['trackDataURL'], trackDbObject['dataType'], trackDbObject['track'], self.myFinalTracksFolderPath)
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70 subtools.add_track_json(self.trackList, trackDbObject['options'])
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71
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72 def terminate(self, debug="false"):
6
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73 """ Write html file """
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74 self._indexName()
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75 if debug.lower() == "false":
6
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76 self._removeRaw()
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77 self._outHtml()
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78 print "Success!\n"
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80
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81 def _customizeHTMLFeature(self, trackDbObject):
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82 if trackDbObject['options']:
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83 subfeatures = trackDbObject['options'].get('subfeatureClasses')
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84 feature_color = trackDbObject['options']['feature_color']
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85 if subfeatures:
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86 for key, value in subfeatures.items():
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87 self.myTrackStyle.addCustomColor(value, feature_color)
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88 else:
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89 customizedFeature = santitizer.sanitize_name(trackDbObject['trackLabel'])
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90 clientConfig = json.loads(trackDbObject['options']['clientConfig'])
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91 clientConfig['renderClassName'] = customizedFeature
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92 trackDbObject['options']['clientConfig'] = json.dumps(clientConfig)
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93 self.myTrackStyle.addCustomColor(customizedFeature, feature_color)
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94
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95 def _removeRaw(self):
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96 if os.path.exists(self.myTracksFolderPath):
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97 shutil.rmtree(self.myTracksFolderPath)
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98
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99 def _createTrackList(self):
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100 if not os.path.exists(self.trackList):
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101 os.mknod(self.trackList)
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102
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103 def _prepareRefseq(self):
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104 subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
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105
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106 def _indexName(self):
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107 subtools.generate_names(self.mySpecieFolderPath)
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108 print "finished name index \n"
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109
6
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110 def _outHtml(self):
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111 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
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112 output_encoding='utf-8', encoding_errors='replace')
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113 htmlTemplate = mylookup.get_template("display.txt")
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114
6
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115 with open(self.outputFile, 'w') as htmlfile:
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116 htmlMakoRendered = htmlTemplate.render(
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117 jbrowse_hub_name = self.reference_genome.assembly_id,
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118 trackList = os.path.relpath(self.trackList, self.extra_files_path)
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119 )
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120 htmlfile.write(htmlMakoRendered)
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121
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122 def __createAssemblyHub__(self, extra_files_path):
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123 # Get all necessaries infos first
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124 # 2bit file creation from input fasta
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125 twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
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126 subtools.faToTwoBit(self.reference_genome.false_path, twoBitFile.name)
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127
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128 # Generate the twoBitInfo
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129 twoBitInfoFile = tempfile.NamedTemporaryFile(bufsize=0)
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130 subtools.twoBitInfo(twoBitFile.name, twoBitInfoFile.name)
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131
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132 # Then we get the output to generate the chromSizes
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133 self.chromSizesFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".chrom.sizes")
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134 subtools.sortChromSizes(twoBitInfoFile.name, self.chromSizesFile.name)
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135
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136 # We can get the biggest scaffold here, with chromSizesFile
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137 with open(self.chromSizesFile.name, 'r') as chrom_sizes:
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138 # TODO: Check if exists
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139 self.default_pos = chrom_sizes.readline().split()[0]
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140
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141 # Create the specie folder, use generic name "myHub", to support display JBrowse with Galaxy display application
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142 mySpecieFolderPath = os.path.join(extra_files_path, "myHub")
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143 if not os.path.exists(mySpecieFolderPath):
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144 os.makedirs(mySpecieFolderPath)
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145 self.mySpecieFolderPath = mySpecieFolderPath
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146
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147 # Create the folder named 'raw' inside the specie folder to place raw files
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148 tracksFolderPath = os.path.join(mySpecieFolderPath, "raw")
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149 if not os.path.exists(tracksFolderPath):
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150 os.makedirs(tracksFolderPath)
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151 self.myTracksFolderPath = tracksFolderPath
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152
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153 # Create the folder tracks into the specie folder
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154 finalTracksFolderPath = os.path.join(mySpecieFolderPath, "tracks")
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155 if not os.path.exists(finalTracksFolderPath):
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156 os.makedirs(finalTracksFolderPath)
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157 self.myFinalTracksFolderPath = finalTracksFolderPath
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158
6
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159 myBinaryFolderPath = os.path.join(mySpecieFolderPath, 'bbi')
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160 if not os.path.exists(myBinaryFolderPath):
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161 os.makedirs(myBinaryFolderPath)
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162 self.myBinaryFolderPath = myBinaryFolderPath