Mercurial > repos > rmarenco > hubarchivecreator
annotate hubArchiveCreator.py @ 22:7ddf651457df draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
author | yating-l |
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date | Wed, 12 Apr 2017 17:03:51 -0400 |
parents | 884ee2a71680 |
children | fcc1021bd496 |
rev | line source |
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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 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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32 |
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33 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort |
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34 |
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35 |
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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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60 |
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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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63 |
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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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66 |
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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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69 |
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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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72 |
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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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81 |
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82 parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs') |
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83 |
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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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85 |
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86 parser.add_argument('--genome_name', help='UCSC Genome Browser assembly ID') |
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87 |
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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 |
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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 |
13
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276 """ |
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277 |
13
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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 |
13
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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 |
1
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325 if __name__ == "__main__": |
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326 logging.getLogger(__name__) |
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327 main(sys.argv) |