Mercurial > repos > rmarenco > hubarchivecreator
annotate hubArchiveCreator.py @ 17:c02720d1afee draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author | rmarenco |
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date | Fri, 30 Sep 2016 15:14:24 -0400 |
parents | 3233451a3bd6 |
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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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17 |
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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 Bed import Bed |
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22 from BigWig import BigWig |
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23 from util.Fasta import Fasta |
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24 from util.Filters import TraceBackFormatter |
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25 from Gff3 import Gff3 |
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26 from Gtf import Gtf |
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27 from Psl import Psl |
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28 from TrackHub import TrackHub |
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29 |
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30 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort |
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31 |
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32 |
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33 def main(argv): |
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34 # Command Line parsing init |
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35 parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.') |
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36 |
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37 # Reference genome mandatory |
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38 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome') |
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39 |
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40 # GFF3 Management |
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41 parser.add_argument('--gff3', action='append', help='GFF3 format') |
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42 |
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43 # GTF Management |
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44 parser.add_argument('--gtf', action='append', help='GTF format') |
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45 |
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46 # Bed4+12 (TrfBig) |
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47 parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as') |
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48 |
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49 # Generic Bed (Blastx transformed to bed) |
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50 parser.add_argument('--bed', action='append', help='Bed generic format') |
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51 |
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52 # BigWig Management |
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53 parser.add_argument('--bigwig', action='append', help='BigWig format') |
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54 |
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55 # Bam Management |
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56 parser.add_argument('--bam', action='append', help='Bam format') |
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57 |
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58 # Psl Management |
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59 parser.add_argument('--psl', action='append', help='Psl format') |
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60 |
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61 # TODO: Check if the running directory can have issues if we run the tool outside |
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62 parser.add_argument('-d', '--directory', |
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63 help='Running tool directory, where to find the templates. Default is running directory') |
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64 parser.add_argument('-u', '--ucsc_tools_path', |
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65 help='Directory where to find the executables needed to run this tool') |
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66 parser.add_argument('-e', '--extra_files_path', |
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67 help='Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive') |
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68 parser.add_argument('-o', '--output', help='Name of the HTML summarizing the content of the Track Hub Archive') |
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69 |
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70 parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs') |
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71 |
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72 parser.add_argument('--user_email', help='Email of the user who launched the Hub Archive Creation') |
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73 |
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74 parser.add_argument('--genome_name', help='UCSC Genome Browser assembly ID') |
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75 |
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76 parser.add_argument('--debug_mode', action='store_true', help='Allow more details about the errors') |
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77 |
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78 # Begin init variables |
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79 |
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80 toolDirectory = '.' |
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81 extra_files_path = '.' |
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82 |
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83 # Get the args passed in parameter |
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84 args = parser.parse_args() |
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85 |
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86 extra_files_path = args.extra_files_path |
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87 toolDirectory = args.directory |
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88 |
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89 #### Logging management #### |
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90 # If we are in Debug mode, also print in stdout the debug dump |
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91 |
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92 configure_logger(extra_files_path=extra_files_path, debug=args.debug_mode) |
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93 |
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94 #### END Logging management #### |
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95 |
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96 array_inputs_reference_genome = json.loads(args.fasta) |
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97 |
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98 # TODO: Replace these with the object Fasta |
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99 input_fasta_file = array_inputs_reference_genome["false_path"] |
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100 input_fasta_file_name = sanitize_name_input(array_inputs_reference_genome["name"]) |
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101 genome_name = sanitize_name_input(args.genome_name) |
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102 |
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103 reference_genome = Fasta(input_fasta_file, |
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104 input_fasta_file_name, genome_name) |
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105 |
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106 user_email = args.user_email |
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107 |
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108 |
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109 # TODO: Use a class to have a better management of the structure of these inputs |
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110 # These inputs are populated in the Galaxy Wrapper xml and are in this format: |
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111 # ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}] |
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112 # EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH} |
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113 array_inputs_bam = args.bam |
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114 array_inputs_bed_generic = args.bed |
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115 array_inputs_bed_simple_repeats = args.bedSimpleRepeats |
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116 array_inputs_bigwig = args.bigwig |
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117 array_inputs_gff3 = args.gff3 |
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118 array_inputs_gtf = args.gtf |
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119 array_inputs_psl = args.psl |
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120 |
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121 outputFile = args.output |
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122 |
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123 json_inputs_data = args.data_json |
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124 |
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125 inputs_data = json.loads(json_inputs_data) |
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126 # We remove the spaces in ["name"] of inputs_data |
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127 sanitize_name_inputs(inputs_data) |
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128 |
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129 # TODO: Check here all the binaries / tools we need. Exception if missing |
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130 |
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131 # Create the Track Hub folder |
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132 trackHub = TrackHub(reference_genome, user_email, outputFile, extra_files_path, toolDirectory) |
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133 |
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134 all_datatype_dictionary = {} |
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135 |
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136 for (inputs, datatype_class) in [ |
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137 (array_inputs_bam, Bam), |
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138 (array_inputs_bed_generic, Bed), |
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139 (array_inputs_bigwig, BigWig), |
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140 (array_inputs_bed_simple_repeats, BedSimpleRepeats), |
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141 (array_inputs_gff3, Gff3), |
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142 (array_inputs_gtf, Gtf), |
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143 (array_inputs_psl, Psl)]: |
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144 if inputs: |
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145 all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data)) |
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146 |
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147 # Create Ordered Dictionary to add the tracks in the tool form order |
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148 all_datatype_ordered_dictionary = collections.OrderedDict(all_datatype_dictionary) |
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149 |
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150 for index, datatypeObject in all_datatype_ordered_dictionary.iteritems(): |
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151 trackHub.addTrack(datatypeObject.track.trackDb) |
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152 |
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153 # We process all the modifications to create the zip file |
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154 #trackHub.createZip() |
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155 |
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156 # We terminate le process and so create a HTML file summarizing all the files |
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157 trackHub.terminate() |
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158 |
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159 logging.debug('#### End of HubArchiveCreator Debug Mode: Bye! ####') |
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160 |
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161 sys.exit(0) |
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162 |
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163 |
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164 def sanitize_name_input(string_to_sanitize): |
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165 return string_to_sanitize \ |
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166 .replace("/", "_") \ |
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167 .replace(" ", "_") |
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168 |
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169 |
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170 def sanitize_name_inputs(inputs_data): |
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171 """ |
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172 Sometimes output from Galaxy, or even just file name from user have spaces |
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173 Also, it can contain '/' character and could break the use of os.path function |
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174 :param inputs_data: dict[string, dict[string, string]] |
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175 :return: |
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176 """ |
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177 for key in inputs_data: |
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178 inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"]) |
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179 |
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180 |
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181 def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data): |
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182 """ |
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183 Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub |
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184 and update the dictionary of datatype |
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185 :param ExtensionClass: T <= Datatype |
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186 :param array_inputs: list[string] |
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187 :param inputs_data: |
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188 """ |
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189 |
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190 datatype_dictionary = {} |
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191 |
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192 # TODO: Optimize this double loop |
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193 for input_false_path in array_inputs: |
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194 for key, data_value in inputs_data.items(): |
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195 if key == input_false_path: |
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196 logging.debug("input_false_path: " + input_false_path) |
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197 logging.debug("data_value: " + str(data_value)) |
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198 extensionObject = ExtensionClass(input_false_path, data_value) |
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199 datatype_dictionary.update({data_value["order_index"]: extensionObject}) |
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200 return datatype_dictionary |
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201 |
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202 def configure_logger(extra_files_path=None, debug=False): |
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203 if not extra_files_path: |
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204 raise Exception("Extra files path is not set. Stopping the application") |
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205 |
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206 |
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207 # All case log: log everything in a .log file |
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208 logger_file_name = ''.join([__name__, '.log']) |
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209 logging_file_path = os.path.join(extra_files_path, logger_file_name) |
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210 |
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211 logging.basicConfig(filename=logging_file_path, level=logging.DEBUG) |
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212 |
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213 log_stdout = logging.StreamHandler(sys.stdout) |
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214 if not debug: |
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215 configure_logger_user(log_stdout) |
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216 else: |
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217 configure_logger_dev(log_stdout) |
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218 |
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219 # stderr configuration |
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220 configure_logger_stderr() |
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221 |
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222 logging.debug('#### Welcome in HubArchiveCreator Debug Mode ####\n') |
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223 |
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224 def configure_logger_user(log_stdout=None): |
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225 """ |
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226 User Logger is defined as following: |
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227 - User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback |
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228 in STDOUT |
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229 - Still access to full, brute and traceback for errors |
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230 in STDERR |
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231 - And further access to debug if needed |
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232 in .log |
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233 :return: |
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234 """ |
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235 if not log_stdout: |
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236 raise Exception("No log_stdout given. Stopping the application") |
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237 |
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238 # stdout for INFO / WARN / ERROR / CRITICAL |
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239 log_stdout.setLevel(logging.INFO) |
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240 |
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241 formatter = TraceBackFormatter('%(message)s') |
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242 |
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243 log_stdout.setFormatter(formatter) |
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244 |
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245 logging.getLogger().addHandler(log_stdout) |
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246 |
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247 def configure_logger_dev(log_stdout=None): |
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248 """ |
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249 Dev Logger is defined as following: |
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250 - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout |
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251 - Still access to full, brute and traceback in stderr for errors |
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252 - And further access to debug if needed |
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253 :return: |
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254 """ |
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255 if not log_stdout: |
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256 raise Exception("No log_stdout given. Stopping the application") |
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257 log_format = '%(message)s' |
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258 |
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259 # stdout and stderr and both identical for INFO / WARN / ERROR / CRITICAL |
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260 log_stdout.setLevel(logging.DEBUG) |
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261 |
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262 formatter = logging.Formatter(log_format) |
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263 |
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264 log_stdout.setFormatter(formatter) |
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265 |
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266 logging.getLogger().addHandler(log_stdout) |
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267 |
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268 def configure_logger_stderr(): |
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269 """ |
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270 Configure what should be logged in stderr |
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271 :return: |
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272 """ |
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273 log_error = logging.StreamHandler(sys.stderr) |
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274 log_error.setLevel(logging.ERROR) |
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275 log_error_format = '%(message)s' |
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276 |
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277 formatter_error = logging.Formatter(log_error_format) |
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278 |
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279 log_error.setFormatter(formatter_error) |
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280 |
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281 logging.getLogger().addHandler(log_error) |
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282 |
1
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283 if __name__ == "__main__": |
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284 logging.getLogger(__name__) |
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285 main(sys.argv) |