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annotate hubArchiveCreator.py @ 7:a030b8023882 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 05d9161e2ac41a34a9ab5b1bb9fc012f6512e1ec
author rmarenco
date Tue, 19 Jul 2016 20:33:12 -0400
parents fcff8e9146e7
children 4f9847539a28
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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 This Galaxy tool permits to prepare your files to be ready for
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6 Assembly Hub visualization.
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7 Program test arguments:
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8 hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html
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9 """
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11 import argparse
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12 import collections
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13 import json
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14 import sys
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16 # Internal dependencies
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17 from TrackHub import TrackHub
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18 from Gff3 import Gff3
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19 from Bam import Bam
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20 from BedSimpleRepeats import BedSimpleRepeats
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21 from Bed import Bed
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22 from BigWig import BigWig
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23 from Gtf import Gtf
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26 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
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29 def main(argv):
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30 # Command Line parsing init
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31 parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.')
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32
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33 # Reference genome mandatory
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34 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')
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36 # GFF3 Management
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37 parser.add_argument('--gff3', action='append', help='GFF3 format')
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38
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39 # GTF Management
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40 parser.add_argument('--gtf', action='append', help='GTF format')
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41
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42 # Bed4+12 (TrfBig)
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43 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')
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45 # Generic Bed (Blastx transformed to bed)
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46 parser.add_argument('--bed', action='append', help='Bed generic format')
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48 # BigWig Management
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49 parser.add_argument('--bigwig', action='append', help='BigWig format')
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51 # Bam Management
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52 parser.add_argument('--bam', action='append', help='Bam format')
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53
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54 # TODO: Check if the running directory can have issues if we run the tool outside
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55 parser.add_argument('-d', '--directory',
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56 help='Running tool directory, where to find the templates. Default is running directory')
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57 parser.add_argument('-u', '--ucsc_tools_path',
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58 help='Directory where to find the executables needed to run this tool')
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59 parser.add_argument('-e', '--extra_files_path',
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60 help='Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive')
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61 parser.add_argument('-o', '--output', help='Name of the HTML summarizing the content of the Track Hub Archive')
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63 parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')
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65 ucsc_tools_path = ''
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67 toolDirectory = '.'
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68 extra_files_path = '.'
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70 # Get the args passed in parameter
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71 args = parser.parse_args()
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73 input_fasta_file = args.fasta
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75 # TODO: Add array for each input because we can add multiple -b for example + filter the data associated
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78 array_inputs_gff3 = args.gff3
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79 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
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80 array_inputs_bed_generic = args.bed
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81 array_inputs_gtf = args.gtf
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82 array_inputs_bam = args.bam
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83 array_inputs_bigwig = args.bigwig
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85 outputFile = args.output
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86 json_inputs_data = args.data_json
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88 json_inputs_data = args.data_json
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90 inputs_data = json.loads(json_inputs_data)
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91 # We remove the spaces in ["name"] of inputs_data
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92 sanitize_name_inputs(inputs_data)
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93
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94 if args.directory:
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95 toolDirectory = args.directory
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96 if args.extra_files_path:
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97 extra_files_path = args.extra_files_path
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98
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99 # TODO: Check here all the binaries / tools we need. Exception is missing
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100
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101 # Create the Track Hub folder
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102 trackHub = TrackHub(input_fasta_file, outputFile, extra_files_path, toolDirectory)
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103
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104 all_datatype_dictionary = {}
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105
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106 # Process Augustus
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107 if array_inputs_gff3:
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108 create_ordered_datatype_objects(Gff3, array_inputs_gff3, inputs_data, input_fasta_file,
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109 extra_files_path, all_datatype_dictionary, toolDirectory)
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110
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111 # Process Bed simple repeats => From Tandem Repeats Finder / TrfBig
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112 if array_inputs_bed_simple_repeats:
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113 create_ordered_datatype_objects(BedSimpleRepeats, array_inputs_bed_simple_repeats, inputs_data, input_fasta_file,
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114 extra_files_path, all_datatype_dictionary, toolDirectory)
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115
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116 # Process a Bed => tBlastN or TopHat
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117 if array_inputs_bed_generic:
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118 create_ordered_datatype_objects(Bed, array_inputs_bed_generic, inputs_data, input_fasta_file,
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119 extra_files_path, all_datatype_dictionary, toolDirectory)
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120
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121 # Process a GTF => Tophat
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122 if array_inputs_gtf:
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123 create_ordered_datatype_objects(Gtf, array_inputs_gtf, inputs_data, input_fasta_file,
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124 extra_files_path, all_datatype_dictionary, toolDirectory)
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125
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126 # Process a Bam => Tophat
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127 if array_inputs_bam:
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128 create_ordered_datatype_objects(Bam, array_inputs_bam, inputs_data, input_fasta_file,
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129 extra_files_path, all_datatype_dictionary, toolDirectory)
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130
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131 # Process a BigWig => From Bam
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132 if array_inputs_bigwig:
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133 create_ordered_datatype_objects(BigWig, array_inputs_bigwig, inputs_data, input_fasta_file,
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134 extra_files_path, all_datatype_dictionary, toolDirectory)
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135
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136 # Create Ordered Dictionary to add the tracks in the tool form order
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137 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)
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138
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139 for index, datatypeObject in all_datatype_ordered_dictionary.iteritems():
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140 trackHub.addTrack(datatypeObject.track.trackDb)
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141
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142 # We process all the modifications to create the zip file
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143 trackHub.createZip()
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144
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145 # We terminate le process and so create a HTML file summarizing all the files
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146 trackHub.terminate()
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147
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148 sys.exit(0)
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149
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150
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151 def sanitize_name_inputs(inputs_data):
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152 """
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153 Sometimes output from Galaxy, or even just file name from user have spaces
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154 Also, it can contain '/' character and could break the use of os.path function
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155 :param inputs_data: dict[string, dict[string, string]]
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156 :return:
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157 """
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158 for key in inputs_data:
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159 inputs_data[key]["name"] = inputs_data[key]["name"]\
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160 .replace("/", "_")\
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161 .replace(" ", "_")
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162
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163
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164 def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data, input_fasta_file,
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165 extra_files_path, all_datatype_dictionary, tool_directory):
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166 """
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167 Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
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168 and update the dictionary of datatype
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169 :param ExtensionClass: T <= Datatype
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170 :param array_inputs: list[string]
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171 :param inputs_data:
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172 :param input_fasta_file: string
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173 :param extra_files_path: string
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174 :param tool_directory; string
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175 """
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176
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177 datatype_dictionary = {}
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178
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179 # TODO: Optimize this double loop
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180 for input_false_path in array_inputs:
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181 for key, data_value in inputs_data.items():
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182 if key == input_false_path:
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183 extensionObject = ExtensionClass(input_false_path, data_value,
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184 input_fasta_file, extra_files_path, tool_directory)
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
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185 datatype_dictionary.update({data_value["order_index"]: extensionObject})
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
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186 all_datatype_dictionary.update(datatype_dictionary)
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
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187
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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188 if __name__ == "__main__":
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
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189 main(sys.argv)