Mercurial > repos > yating-l > jbrowse_hub

annotate jbrowse_hub.py @ 0:e4f3f2ed4fa5 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
author yating-l
date Fri, 10 Mar 2017 13:48:19 -0500
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children e7c80e9b70ae
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0
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1 #!/usr/bin/env python
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2
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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
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14 def main(argv):
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15 parser = argparse.ArgumentParser(description='Create a hub to display in jbrowse.')
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16
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17 # Reference genome mandatory
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18 parser.add_argument('-f', '--fasta', help='Fasta file of the reference genome')
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19
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20 # Output folder
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21 parser.add_argument('-o', '--out', help='Name of the HTML summarizing the content of the JBrowse Hub')
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22
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23 # GFF3
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24 parser.add_argument('--gff3', action='append', help='GFF3 format')
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25
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26 # trfBig simple repeats (BED 4+12)
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27 parser.add_argument('--bedSimpleRepeats', action='append', help='BED 4+12 format, using simpleRepeats.as')
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28
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29 # regtools (BED 12+1)
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30 parser.add_argument('--bedSpliceJunctions', action='append', help='BED 12+1 format, using spliceJunctions.as')
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31
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32 # tblastn alignment (blastxml)
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33 parser.add_argument('--blastxml', action='append', help='blastxml format from tblastn')
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34
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35 # BAM format
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36 parser.add_argument('--bam', action='append', help='BAM format from HISAT')
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37 # put bam index file at the same directory with bam file
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38 # parser.add_argument('--bai', action='append', help='BAM index format from HISAT')
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39
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40 # BIGWIG format
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41 parser.add_argument('--bigwig', action='append', help='BIGWIG format to show rnaseq coverage')
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42
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43 # GTF format
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44 parser.add_argument('--gtf', action='append', help='GTF format from StringTie')
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45
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46 args = parser.parse_args()
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47 all_datatype_dictionary = dict()
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48 all_tracks = []
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49
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50 reference = args.fasta
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51 out_path = args.out
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52 tool_directory = 'JBrowse-1.12.1/bin'
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53 chrom_size = utils.getChromSizes(reference, '../ucsc_tools_340_for_HAC')
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54 array_inputs_bam = args.bam
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55 array_inputs_bed_simple_repeats = args.bedSimpleRepeats
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56 array_inputs_bed_splice_junctions = args.bedSpliceJunctions
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57 array_inputs_bigwig = args.bigwig
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58 array_inputs_gff3 = args.gff3
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59 array_inputs_gtf = args.gtf
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60 array_inputs_blastxml = args.blastxml
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61 if array_inputs_bam:
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62 all_datatype_dictionary['bam'] = array_inputs_bam
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63 if array_inputs_bed_simple_repeats:
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64 all_datatype_dictionary['bedSimpleRepeats'] = array_inputs_bed_simple_repeats
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65 if array_inputs_bed_splice_junctions:
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66 all_datatype_dictionary['bedSpliceJunctions'] = array_inputs_bed_splice_junctions
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67 if array_inputs_bigwig:
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68 all_datatype_dictionary['bigwig'] = array_inputs_bigwig
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69 if array_inputs_gff3:
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70 all_datatype_dictionary['gff3'] = array_inputs_gff3
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71 if array_inputs_gtf:
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72 all_datatype_dictionary['gtf'] = array_inputs_gtf
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73 if array_inputs_blastxml:
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74 all_datatype_dictionary['blastxml'] = array_inputs_blastxml
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75
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76 print all_datatype_dictionary
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77
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78 for datatype, inputfiles in all_datatype_dictionary.items():
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79 try:
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80 user_input = inputfiles
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81 if not user_input:
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82 raise ValueError('empty input, must provide track files!\n')
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83 except IOError:
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84 print 'Cannot open', datatype
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85 else:
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86 for f in inputfiles:
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87 track = trackObject.trackObject(f, datatype, chrom_size.name)
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88 track.addToRaw()
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89 all_tracks.append(track)
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90
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91 jbrowseHub = TrackHub.TrackHub(all_tracks, reference, out_path, tool_directory)
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92 jbrowseHub.createHub()
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93
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94
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95 '''
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96 if reference:
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97 p = subprocess.Popen(['JBrowse-1.12.1/bin/prepare-refseqs.pl', '--fasta', reference, '--out', out_path])
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98 # Wait for process to terminate.
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99 p.communicate()
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yating-l
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100 else:
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yating-l
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101 parser.print_help()
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yating-l
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102
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yating-l
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103
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104 if input_simple_repeats:
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yating-l
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105 bedToGff3(input_simple_repeats, chrom_size, 'trfbig', 'repeats.gff3')
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yating-l
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106 label = "repeats"
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yating-l
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107 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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yating-l
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108 p.communicate()
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109 if input_splice_junctions:
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yating-l
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110 bedToGff3(input_splice_junctions, chrom_size, 'regtools', 'regtools.gff3')
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111 label = "regtools"
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112 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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113 p.communicate()
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114 attr = dict()
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115 track = dict()
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116 attr['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
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117 track['regtools'] = attr
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118 json_file = os.path.join(out_path, "trackList.json")
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119 utils.add_tracks_to_json(json_file, track, 'add_attr')
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120 if blastxml:
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121 blastxmlToGff3.blastxml2gff3(blastxml, "blast.gff3")
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122 label = "blast"
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123 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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yating-l
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124 p.communicate()
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125 if array_inputs_gff3:
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126 for gff3 in array_inputs_gff3:
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127 label = os.path.basename(gff3)
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128 label = label.replace('.', '_')
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129 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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yating-l
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130 p.communicate()
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yating-l
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131 if 'Augustus' in label:
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132 attr = dict()
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133 track = dict()
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134 attr['transcriptType'] = 'transcript'
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135 track['Augustus'] = attr
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136 json_file = os.path.join(out_path, "trackList.json")
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yating-l
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137 utils.add_tracks_to_json(json_file, track, 'add_attr')
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138 if bam:
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139 json_file = os.path.join(out_path, "trackList.json")
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yating-l
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140 bam_track = dict()
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141 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
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yating-l
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142 bam_track['label'] = 'alignments'
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143 bam_track['urlTemplate'] = '../raw/HISAT_on_data_3,_data_2,_and_data_1.bam'
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yating-l
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144 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
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145 print "add bam track\n"
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146 if bigwig:
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147 json_file = os.path.join(out_path, "trackList.json")
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148 bigwig_track = dict()
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149 bigwig_track['label'] = 'rnaseq'
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150 bigwig_track['key'] = 'RNA-Seq Coverage'
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151 bigwig_track['urlTemplate'] = '../raw/Convert_Bam_to_BigWig_on_data_3_and_data_15.bigwig'
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152 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
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153 bigwig_track['variance_band'] = True
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154 bigwig_track['style'] = dict()
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155 bigwig_track['style']['pos_color'] = '#FFA600'
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156 bigwig_track['style']['neg_color'] = '#005EFF'
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157 bigwig_track['style']['clip_marker_color'] = 'red'
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158 bigwig_track['style']['height'] = 100
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yating-l
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159 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
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160
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161 if gtf:
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162 utils.gtfToGff3(gtf, 'stringtie.gff3', chrom_size)
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163 label = os.path.basename('stringtie')
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164 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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165 p.communicate()
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166 attr = dict()
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167 track = dict()
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168 attr['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
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169 track['stringtie'] = attr
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170 json_file = os.path.join(out_path, "trackList.json")
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171 utils.add_tracks_to_json(json_file, track, 'add_attr')
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172
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173 # Index name, it takes a long time, exclude it for now
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174 p = subprocess.Popen(['JBrowse-1.12.1/bin/generate-names.pl', '-v', '--out', out_path])
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175 p.communicate()
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176 print "finished name index \n"
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177 '''
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178
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179 if __name__ == "__main__":
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180 main(sys.argv)
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181