Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.py @ 16:f2285f29a6fa draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Tue, 14 Mar 2017 15:15:54 -0400
parents e1f188b43750
children a4a54b925c73
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1 #!/usr/bin/env python
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3 import os
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4 import sys
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5 import argparse
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6 import subprocess
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7 from bedToGff3 import bedToGff3
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8 import blastxmlToGff3
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9 import utils
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10 import tempfile
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11 import trackObject
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12 import TrackHub
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13 import shutil
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15 def main(argv):
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16 parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')
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18 # Reference genome mandatory
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19 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')
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21 # Genome name
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22 parser.add_argument('-g', '--genome_name', help='Name of reference genome')
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24 # Output folder
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25 parser.add_argument('-o', '--out', help='output html')
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27 # Output folder
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28 parser.add_argument('-e', '--extra_files_path', help="Directory of JBrowse Hub folder")
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30 # GFF3 structure: gene->transcription->CDS
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31 parser.add_argument('--gff3_transcript', action='append', help='GFF3 format, structure: gene->transcription->CDS')
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33 # GFF3 structure: gene->mRNA->CDS
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34 parser.add_argument('--gff3_mrna', action='append', help='GFF3 format, structure: gene->mRNA->CDS')
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36 # trfBig simple repeats (BED 4+12)
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37 parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')
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39 # regtools (BED 12+1)
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40 parser.add_argument('--bedSpliceJunctions', action='append', help='BED 12+1 format, using spliceJunctions.as')
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42 # tblastn alignment (blastxml)
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43 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn')
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45 # BAM format
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46 parser.add_argument('--bam', action='append', help='BAM format from HISAT')
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47 # put bam index file at the same directory with bam file
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48 parser.add_argument('--bai', action='append', help='BAM index format from HISAT')
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50 # BIGWIG format
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51 parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')
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53 # GTF format
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54 parser.add_argument('--gtf', action='append', help='GTF format from StringTie')
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56 args = parser.parse_args()
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57 all_datatype_dictionary = dict()
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60 reference = args.fasta
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61 genome = 'unknown'
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62 out_path = '.'
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63 extra_files_path = '.'
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64 if args.genome_name:
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65 genome = utils.sanitize_name_path(args.genome_name)
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66 if args.out:
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67 out_path = args.out
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68 if args.extra_files_path:
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69 extra_files_path = utils.sanitize_name_path(args.extra_files_path)
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70 cwd = os.getcwd()
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71 #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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72 tool_directory = os.path.join(cwd, 'JBrowse-1.12.1/bin')
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73 chrom_size = utils.getChromSizes(reference, tool_directory)
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74 all_tracks = trackObject.trackObject(chrom_size.name, genome, extra_files_path) #store converted files in the array: all_tracks.tracks
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75 array_inputs_bam = args.bam
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76 array_inputs_bai = args.bai
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77 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
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78 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
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79 array_inputs_bigwig = args.bigwig
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80 array_inputs_gff3_transcript = args.gff3_transcript
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81 array_inputs_gff3_mrna = args.gff3_mrna
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82 array_inputs_gtf = args.gtf
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83 array_inputs_blastxml = args.blastxml
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84 if array_inputs_bam:
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85 all_datatype_dictionary['bam'] = array_inputs_bam
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86 if array_inputs_bai:
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87 all_datatype_dictionary['bai'] = array_inputs_bai
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88 if array_inputs_bed_simple_repeats:
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89 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
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90 if array_inputs_bed_splice_junctions:
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91 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
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92 if array_inputs_bigwig:
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93 all_datatype_dictionary['bigwig'] = array_inputs_bigwig
12
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94 if array_inputs_gff3_transcript:
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95 all_datatype_dictionary['gff3_transcript'] = array_inputs_gff3_transcript
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96 if array_inputs_gff3_mrna:
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97 all_datatype_dictionary['gff3_mrna'] = array_inputs_gff3_mrna
0
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98 if array_inputs_gtf:
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99 all_datatype_dictionary['gtf'] = array_inputs_gtf
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100 if array_inputs_blastxml:
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101 all_datatype_dictionary['blastxml'] = array_inputs_blastxml
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102
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103 print all_datatype_dictionary
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104
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105 for datatype, inputfiles in all_datatype_dictionary.items():
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106 try:
5
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107 if not inputfiles:
0
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108 raise ValueError('empty input, must provide track files!\n')
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109 except IOError:
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110 print 'Cannot open', datatype
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111 else:
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112 for f in inputfiles:
5
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113 all_tracks.addToRaw(f, datatype)
0
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114
5
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115 jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory, genome, extra_files_path)
0
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116 jbrowseHub.createHub()
5
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117
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118
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119
0
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120 '''
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121 if reference:
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122 p = subprocess.Popen(['JBrowse-1.12.1/bin/prepare-refseqs.pl', '--fasta', reference, '--out', out_path])
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123 # Wait for process to terminate.
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124 p.communicate()
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125 else:
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126 parser.print_help()
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127
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128
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129 if input_simple_repeats:
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130 bedToGff3(input_simple_repeats, chrom_size, 'trfbig', 'repeats.gff3')
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131 label = "repeats"
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132 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'repeats.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
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133 p.communicate()
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134 if input_splice_junctions:
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135 bedToGff3(input_splice_junctions, chrom_size, 'regtools', 'regtools.gff3')
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136 label = "regtools"
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137 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'regtools.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
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yating-l
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138 p.communicate()
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139 attr = dict()
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140 track = dict()
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141 attr['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
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142 track['regtools'] = attr
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143 json_file = os.path.join(out_path, "trackList.json")
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144 utils.add_tracks_to_json(json_file, track, 'add_attr')
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145 if blastxml:
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146 blastxmlToGff3.blastxml2gff3(blastxml, "blast.gff3")
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147 label = "blast"
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148 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'blast.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
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149 p.communicate()
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150 if array_inputs_gff3:
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151 for gff3 in array_inputs_gff3:
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152 label = os.path.basename(gff3)
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153 label = label.replace('.', '_')
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154 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', gff3, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
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155 p.communicate()
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156 if 'Augustus' in label:
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157 attr = dict()
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158 track = dict()
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159 attr['transcriptType'] = 'transcript'
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160 track['Augustus'] = attr
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161 json_file = os.path.join(out_path, "trackList.json")
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162 utils.add_tracks_to_json(json_file, track, 'add_attr')
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163 if bam:
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164 json_file = os.path.join(out_path, "trackList.json")
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165 bam_track = dict()
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166 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
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167 bam_track['label'] = 'alignments'
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168 bam_track['urlTemplate'] = '../raw/HISAT_on_data_3,_data_2,_and_data_1.bam'
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169 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
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170 print "add bam track\n"
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171 if bigwig:
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172 json_file = os.path.join(out_path, "trackList.json")
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173 bigwig_track = dict()
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174 bigwig_track['label'] = 'rnaseq'
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175 bigwig_track['key'] = 'RNA-Seq Coverage'
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176 bigwig_track['urlTemplate'] = '../raw/Convert_Bam_to_BigWig_on_data_3_and_data_15.bigwig'
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177 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
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178 bigwig_track['variance_band'] = True
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179 bigwig_track['style'] = dict()
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180 bigwig_track['style']['pos_color'] = '#FFA600'
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181 bigwig_track['style']['neg_color'] = '#005EFF'
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182 bigwig_track['style']['clip_marker_color'] = 'red'
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183 bigwig_track['style']['height'] = 100
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184 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
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185
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186 if gtf:
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187 utils.gtfToGff3(gtf, 'stringtie.gff3', chrom_size)
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188 label = os.path.basename('stringtie')
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189 p = subprocess.Popen(['JBrowse-1.12.1/bin/flatfile-to-json.pl', '--gff', 'stringtie.gff3', '--trackType', 'CanvasFeatures', '--trackLabel', label, '--out', out_path])
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190 p.communicate()
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191 attr = dict()
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192 track = dict()
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193 attr['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
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194 track['stringtie'] = attr
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195 json_file = os.path.join(out_path, "trackList.json")
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196 utils.add_tracks_to_json(json_file, track, 'add_attr')
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197
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198 # Index name, it takes a long time, exclude it for now
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199 p = subprocess.Popen(['JBrowse-1.12.1/bin/generate-names.pl', '-v', '--out', out_path])
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200 p.communicate()
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201 print "finished name index \n"
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202 '''
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203
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204 if __name__ == "__main__":
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205 main(sys.argv)
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206