Mercurial > repos > yating-l > hubarchivecreator

annotate hubArchiveCreator.py @ 52:c66803bff0cc draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
author yating-l
date Thu, 11 May 2017 17:21:15 -0400
parents 364b8db8de17
children 4a58094b051e
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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 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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10
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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 logging
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15 import os
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16 import sys
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18 # Internal dependencies
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19 from Bam import Bam
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20 from BedSimpleRepeats import BedSimpleRepeats
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21 from BedSpliceJunctions import BedSpliceJunctions
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22 from Bed import Bed
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23 from BigWig import BigWig
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24 from util.Fasta import Fasta
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25 from util.Filters import TraceBackFormatter
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26 from Gff3 import Gff3
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27 from Gtf import Gtf
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28 from Psl import Psl
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29 from TrackHub import TrackHub
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30 from bigPsl import bigPsl
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31 from BedBlastAlignments import BedBlastAlignments
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33 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
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36 def main(argv):
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37 # Command Line parsing init
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38 parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.')
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39
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40 # Reference genome mandatory
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41 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')
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42
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43 # GFF3 Management
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44 parser.add_argument('--gff3', action='append', help='GFF3 format')
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45
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46 # GTF Management
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47 parser.add_argument('--gtf', action='append', help='GTF format')
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48
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49 # Bed4+12 (TrfBig)
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50 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')
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51
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52 # Bed12+1 (regtools)
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53 parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')
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54
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55 # Generic Bed (Blastx transformed to bed)
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56 parser.add_argument('--bed', action='append', help='Bed generic format')
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57
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58 # BigPsl (blat alignment)
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59 parser.add_argument('--bigpsl', action='append', help='bigPsl format, using bigPsl.as')
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61 # Bed12+12 (tblastn alignment)
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62 parser.add_argument('--bedBlastAlignments', action='append', help='Bed12+12 format, using bigPsl.as')
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64 # BigWig Management
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65 parser.add_argument('--bigwig', action='append', help='BigWig format')
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67 # Bam Management
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68 parser.add_argument('--bam', action='append', help='Bam format')
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70 # Psl Management
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71 parser.add_argument('--psl', action='append', help='Psl format')
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73 # TODO: Check if the running directory can have issues if we run the tool outside
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74 parser.add_argument('-d', '--directory',
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75 help='Running tool directory, where to find the templates. Default is running directory')
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76 parser.add_argument('-u', '--ucsc_tools_path',
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77 help='Directory where to find the executables needed to run this tool')
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78 parser.add_argument('-e', '--extra_files_path',
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79 help='Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive')
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80 parser.add_argument('-o', '--output', help='Name of the HTML summarizing the content of the Track Hub Archive')
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82 parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')
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84 parser.add_argument('--user_email', help='Email of the user who launched the Hub Archive Creation')
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86 parser.add_argument('--genome_name', help='UCSC Genome Browser assembly ID')
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88 parser.add_argument('--debug_mode', action='store_true', help='Allow more details about the errors')
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89
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90 # Begin init variables
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91
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92 toolDirectory = '.'
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93 extra_files_path = '.'
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94
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95 # Get the args passed in parameter
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96 args = parser.parse_args()
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97
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98 extra_files_path = args.extra_files_path
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99 toolDirectory = args.directory
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100
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101 #### Logging management ####
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102 # If we are in Debug mode, also print in stdout the debug dump
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103
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104 configure_logger(extra_files_path=extra_files_path, debug=args.debug_mode)
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105
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106 #### END Logging management ####
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107
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108 array_inputs_reference_genome = json.loads(args.fasta)
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109
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110 # TODO: Replace these with the object Fasta
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111 input_fasta_file = array_inputs_reference_genome["false_path"]
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112 input_fasta_file_name = sanitize_name_input(array_inputs_reference_genome["name"])
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113 genome_name = sanitize_name_input(args.genome_name)
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114
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115 reference_genome = Fasta(input_fasta_file,
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116 input_fasta_file_name, genome_name)
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117
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118 user_email = args.user_email
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119
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120
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121 # TODO: Use a class to have a better management of the structure of these inputs
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122 # These inputs are populated in the Galaxy Wrapper xml and are in this format:
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123 # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]
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124 # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}
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125 array_inputs_bam = args.bam
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126 array_inputs_bed_generic = args.bed
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127 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
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128 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
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129 array_inputs_bigwig = args.bigwig
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130 array_inputs_gff3 = args.gff3
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131 array_inputs_gtf = args.gtf
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132 array_inputs_psl = args.psl
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133 array_inputs_bigpsl = args.bigpsl
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134 array_inputs_bed_blast_alignments = args.bedBlastAlignments
11
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135
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136 outputFile = args.output
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137
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138 json_inputs_data = args.data_json
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139
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140 # TODO: Instead use a class to properly store the objects, with object_hook
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141 inputs_data = json.loads(json_inputs_data)
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142 # We remove the spaces in ["name"] of inputs_data
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143 sanitize_name_inputs(inputs_data)
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144
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145 # TODO: Check here all the binaries / tools we need. Exception if missing
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146
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147 # Create the Track Hub folder
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148 trackHub = TrackHub(reference_genome, user_email, outputFile, extra_files_path, toolDirectory)
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149
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150 all_datatype_dictionary = {}
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151
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152 for (inputs, datatype_class) in [
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153 (array_inputs_bam, Bam),
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154 (array_inputs_bed_generic, Bed),
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155 (array_inputs_bigwig, BigWig),
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156 (array_inputs_bed_simple_repeats, BedSimpleRepeats),
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157 (array_inputs_bed_splice_junctions, BedSpliceJunctions),
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158 (array_inputs_gff3, Gff3),
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159 (array_inputs_gtf, Gtf),
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160 (array_inputs_psl, Psl),
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161 (array_inputs_bigpsl, bigPsl),
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162 (array_inputs_bed_blast_alignments, BedBlastAlignments)]:
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163 if inputs:
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164 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))
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165
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166 # Create Ordered Dictionary to add the tracks in the tool form order
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167 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary)
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168
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169 logging.debug("----- End of all_datatype_dictionary processing -----")
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170 logging.debug("all_datatype_ordered_dictionary keys are: {0}".format(all_datatype_ordered_dictionary.values()))
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171
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172 logging.debug("----- Beginning of Track adding processing -----")
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173 for index, datatypeObject in all_datatype_ordered_dictionary.iteritems():
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174 trackHub.addTrack(datatypeObject.track.trackDb)
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175 logging.debug("----- End of Track adding processing -----")
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176
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177 # We process all the modifications to create the zip file
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178 #trackHub.createZip()
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179
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180 # We terminate le process and so create a HTML file summarizing all the files
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181 trackHub.terminate()
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182
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183 logging.debug('#### End of HubArchiveCreator Debug Mode: Bye! ####')
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184
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185 sys.exit(0)
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186
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187
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188 def sanitize_name_input(string_to_sanitize):
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189 """
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190 Sanitize the string passed in parameter by replacing '/' and ' ' by '_'
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191
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192 :param string_to_sanitize:
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193 :return :
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194
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195 :Example:
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196
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197 >>> sanitize_name_input('this/is an//example')
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198 this_is_an__example
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199 """
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200 return string_to_sanitize \
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201 .replace("/", "_") \
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202 .replace(" ", "_")
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203
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204
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205 def sanitize_name_inputs(inputs_data):
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206 """
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207 Sanitize value of the keys "name" of the dictionary passed in parameter.
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208
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209 Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.
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210 Also, it can contain '/' character and could break the use of os.path function.
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211
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212 :param inputs_data: dict[string, dict[string, string]]
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213 """
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214 for key in inputs_data:
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215 inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])
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216
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217
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218 def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data):
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219 """
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220 Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
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221 and update the dictionary of datatype
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222
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223 :param ExtensionClass:
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224 :param array_inputs:
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225 :param inputs_data:
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226 :type ExtensionClass: Datatype
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227 :type array_inputs: list[string]
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228 :type inputs_data: dict
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229 :rtype: dict
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230 """
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231
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232 datatype_dictionary = {}
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233
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234 # TODO: Optimize this double loop
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235 for input_false_path in array_inputs:
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236 for key, data_value in inputs_data.items():
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237 if key == input_false_path:
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238 logging.debug("input_false_path: " + input_false_path)
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239 logging.debug("data_value: " + str(data_value))
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240 extensionObject = ExtensionClass(input_false_path, data_value)
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241 datatype_dictionary.update({data_value["order_index"]: extensionObject})
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242 return datatype_dictionary
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243
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244 def configure_logger(extra_files_path=None, debug=False):
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245 if not extra_files_path:
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246 raise Exception("Extra files path is not set. Stopping the application")
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247
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248
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249 # All case log: log everything in a .log file
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250 logger_file_name = ''.join([__name__, '.log'])
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251 logging_file_path = os.path.join(extra_files_path, logger_file_name)
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252
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253 logging.basicConfig(filename=logging_file_path, level=logging.DEBUG)
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254
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255 log_stdout = logging.StreamHandler(sys.stdout)
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256 if not debug:
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257 configure_logger_user(log_stdout)
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258 else:
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259 configure_logger_dev(log_stdout)
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260
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261 # stderr configuration
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262 configure_logger_stderr()
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263
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264 logging.debug('#### Welcome in HubArchiveCreator Debug Mode ####\n')
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265
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266 def configure_logger_user(log_stdout=None):
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267 """
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268 User Logger is defined as following:
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269 - User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback
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270 in STDOUT
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271 - Still access to full, brute and traceback for errors
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272 in STDERR
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273 - And further access to debug if needed
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274 in .log
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275
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276 """
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277
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278 if not log_stdout:
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279 raise Exception("No log_stdout given. Stopping the application")
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280
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281 # stdout for INFO / WARN / ERROR / CRITICAL
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282 log_stdout.setLevel(logging.INFO)
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283
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284 formatter = TraceBackFormatter('%(message)s')
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285
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286 log_stdout.setFormatter(formatter)
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287
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288 logging.getLogger().addHandler(log_stdout)
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289
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290 def configure_logger_dev(log_stdout=None):
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291 """
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292 Dev Logger is defined as following:
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293 - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout
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294 - Still access to full, brute and traceback in stderr for errors
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295 - And further access to debug if needed
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296
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297 """
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298 if not log_stdout:
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299 raise Exception("No log_stdout given. Stopping the application")
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300 log_format = '%(message)s'
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301
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302 # stdout and stderr and both identical for INFO / WARN / ERROR / CRITICAL
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303 log_stdout.setLevel(logging.DEBUG)
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304
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305 formatter = logging.Formatter(log_format)
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306
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307 log_stdout.setFormatter(formatter)
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308
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309 logging.getLogger().addHandler(log_stdout)
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310
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311 def configure_logger_stderr():
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312 """
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313 Configure what should be logged in stderr
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314 """
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315 log_error = logging.StreamHandler(sys.stderr)
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316 log_error.setLevel(logging.ERROR)
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317 log_error_format = '%(message)s'
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318
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319 formatter_error = logging.Formatter(log_error_format)
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320
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321 log_error.setFormatter(formatter_error)
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322
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323 logging.getLogger().addHandler(log_error)
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324
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325 if __name__ == "__main__":
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326 logging.getLogger(__name__)
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327 main(sys.argv)