Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.py @ 62:86d6f50870dd draft default tip

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 79699b5964c673b7eb815b4d669ab7f07ea2068a-dirty
author yating-l
date Tue, 11 Apr 2017 16:08:57 -0400
parents ed17bb465bde
children
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1 #!/usr/bin/env python
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3 import sys
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4 import argparse
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5 import json
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6 import utils
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7 import trackObject
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8 import TrackHub
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12 def main(argv):
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13 parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')
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15 # Reference genome mandatory
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16 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome (Required)')
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18 # Genome name
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19 parser.add_argument('-g', '--genome_name', help='Name of reference genome')
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21 # Output folder
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22 parser.add_argument('-o', '--out', help='output html')
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24 # Output folder
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25 parser.add_argument('-e', '--extra_files_path', help='Directory of JBrowse Hub folder')
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27 #Tool Directory
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28 parser.add_argument('-d', '--tool_directory', help='The directory of JBrowse file convertion scripts and UCSC tools')
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30 #GFF3
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31 parser.add_argument('--gff3', action='append', help='GFF3 format')
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33 # GFF3 structure: gene->transcription->CDS
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34 parser.add_argument('--gff3_transcript', action='append', help='GFF3 format for gene prediction, structure: gene->transcription->CDS')
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36 # GFF3 structure: gene->mRNA->CDS
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37 parser.add_argument('--gff3_mrna', action='append', help='GFF3 format for gene prediction, structure: gene->mRNA->CDS')
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39 # generic BED
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40 parser.add_argument('--bed', action='append', help='BED format')
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42 # trfBig simple repeats (BED 4+12)
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43 parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')
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45 # regtools (BED 12+1)
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46 parser.add_argument('--bedSpliceJunctions', action='append', help='BED 12+1 format, using spliceJunctions.as')
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48 # tblastn alignment (blastxml)
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49 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn')
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51 # BAM format
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52 parser.add_argument('--bam', action='append', help='BAM format from HISAT')
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54 # BIGWIG format
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55 parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')
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57 # GTF format
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58 parser.add_argument('--gtf', action='append', help='GTF format from StringTie')
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59
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60 # Metadata json format
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61 parser.add_argument('-j', '--data_json', help='Json containing the metadata of the inputs')
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63 #JBrowse host
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64 parser.add_argument('--jbrowse_host', help="JBrowse Host")
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66 args = parser.parse_args()
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67 all_datatype_dictionary = dict()
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70 if not args.fasta:
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71 parser.print_help()
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72 raise RuntimeError("No reference genome\n")
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73 reference = args.fasta
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74 genome = 'unknown'
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75 out_path = 'unknown.html'
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76 extra_files_path = '.'
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77 tool_directory = '.'
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78 jbrowse_host = ''
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79 if args.jbrowse_host:
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80 jbrowse_host = args.jbrowse_host
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81 if args.genome_name:
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82 genome = args.genome_name
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83 if args.out:
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84 out_path = args.out
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85 if args.extra_files_path:
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86 extra_files_path = args.extra_files_path
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87
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88 #tool_directory not work for Galaxy tool, all tools need to exist in the current PATH, deal with it with tool dependencies
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89 if args.tool_directory:
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90 tool_directory = args.tool_directory
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92 #Calculate chromsome sizes using genome reference and uscs tools
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93 chrom_size = utils.getChromSizes(reference, tool_directory)
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94
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95 #get metadata from json file
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96 json_inputs_data = args.data_json
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97 if json_inputs_data:
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98 inputs_data = json.loads(json_inputs_data)
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99 else:
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100 inputs_data = {}
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101
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102 #print inputs_data
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103
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104 #Initate trackObject
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105 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path)
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106
0
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107 array_inputs_bam = args.bam
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108 array_inputs_bed = args.bed
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109 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
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110 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
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111 array_inputs_bigwig = args.bigwig
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112 array_inputs_gff3 = args.gff3
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113 array_inputs_gff3_transcript = args.gff3_transcript
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114 array_inputs_gff3_mrna = args.gff3_mrna
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115 array_inputs_gtf = args.gtf
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116 array_inputs_blastxml = args.blastxml
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117
0
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118 if array_inputs_bam:
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119 all_datatype_dictionary['bam'] = array_inputs_bam
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120 if array_inputs_bed:
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121 all_datatype_dictionary['bed'] = array_inputs_bed
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122 if array_inputs_bed_simple_repeats:
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123 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
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124 if array_inputs_bed_splice_junctions:
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125 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
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126 if array_inputs_bigwig:
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127 all_datatype_dictionary['bigwig'] = array_inputs_bigwig
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128 if array_inputs_gff3:
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129 all_datatype_dictionary['gff3'] = array_inputs_gff3
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130 if array_inputs_gff3_transcript:
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131 all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript
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132 if array_inputs_gff3_mrna:
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133 all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna
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134 if array_inputs_gtf:
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135 all_datatype_dictionary['gtf'] = array_inputs_gtf
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136 if array_inputs_blastxml:
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137 all_datatype_dictionary['blastxml'] = array_inputs_blastxml
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138
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139 print "input tracks: \n", all_datatype_dictionary
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140
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141 for datatype, inputfiles in all_datatype_dictionary.items():
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142 try:
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143 if not inputfiles:
0
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144 raise ValueError('empty input, must provide track files!\n')
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145 except IOError:
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146 print 'Cannot open', datatype
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147 else:
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148 for f in inputfiles:
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149 #metadata = {}
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150 #print f
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151 #if f in inputs_data.keys():
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152 # metadata = inputs_data[f]
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153 #print metadata
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154 #Convert tracks into gff3 format
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155 all_tracks.addToRaw(f, datatype)
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156
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157 jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path, inputs_data, jbrowse_host)
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158 jbrowseHub.createHub()
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159
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160 """
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161 def extractMetadata(array_inputs, inputs_data):
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162 metadata_dict = {}
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163 for input_false_path in array_inputs:
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164 for key, data_value in inputs_data.items():
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165 if key == input_false_path:
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166 metadata_dict[input_false_path]
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167 """
0
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168
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169 if __name__ == "__main__":
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170 main(sys.argv)
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171