Mercurial > repos > yating-l > jbrowse_hub

annotate TrackHub.py @ 49:193e94a43f0f draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 88aa9133c8eccdb21dbc755eb9643c9e7b09449e-dirty
author yating-l
date Wed, 29 Mar 2017 14:46:23 -0400
parents 6803152ea92a
children 3e5b6f6a9abe
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1 #!/usr/bin/env python
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3 import os
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4 import subprocess
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5 import shutil
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6 import utils
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7
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9 class TrackHub:
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10 def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData):
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11 self.input_files = inputFiles.tracks
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12 self.outfile = outputDirect
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13 self.outfolder = extra_files_path
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14 self.out_path = os.path.join(extra_files_path, genome)
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15 self.reference = reference
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16 self.tool_dir = tool_dir
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17 self.metaData = metaData
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18 self.raw = os.path.join(self.out_path, 'raw')
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19 self.json = os.path.join(self.out_path, 'json')
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20 try:
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21 if os.path.exists(self.json):
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22 shutil.rmtree(self.json)
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23 os.makedirs(self.json)
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24 except OSError as e:
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25 print "Cannot create json folder error({0}): {1}".format(e.errno, e.strerror)
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26 else:
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27 print "Create jbrowse folder {}".format(self.out_path)
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29 def createHub(self):
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30 self.prepareRefseq()
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31 for input_file in self.input_files:
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32 self.addTrack(input_file)
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33 self.indexName()
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34 self.makeArchive()
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35 self.outHtml()
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36 print "Success!\n"
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38 def prepareRefseq(self):
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39 try:
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40 #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
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41 p = subprocess.Popen(['prepare-refseqs.pl', '--fasta', self.reference, '--out', self.json])
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42 # Wait for process to terminate.
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43 p.communicate()
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44 except OSError as e:
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45 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
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46 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
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47 def addTrack(self, track):
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48 #print "false_path" , track['false_path']
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49 if track['false_path'] in self.metaData.keys():
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50 metadata = self.metaData[track['false_path']]
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51 else:
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52 metadata = {}
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53 self.SetMetadata(track, metadata)
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54 if track['dataType'] == 'bam':
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55 self.Bam(track, metadata)
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56 # print "add bam track\n"
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57 elif track['dataType'] == 'bigwig':
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58 self.BigWig(track, metadata)
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59 else:
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60 gff3_file = os.path.join(self.raw, track['fileName'])
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61 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf' or track['dataType'] == 'blastxml':
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62 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
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63 elif track['dataType'] == 'gff3_transcript':
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64 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"transcriptType": "transcript", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
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65 else:
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66 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
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67 p.communicate()
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69 def indexName(self):
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70 p = subprocess.Popen(['generate-names.pl', '-v', '--out', self.json])
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71 p.communicate()
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72 print "finished name index \n"
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74 def makeArchive(self):
49
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75 shutil.make_archive(self.out_path, 'zip', self.out_path)
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76 data_folder = '/var/www/html/JBrowse-1.12.1/jbrowse_hub'
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77 try:
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78 if os.path.exists(data_folder):
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79 if os.path.isdir(data_folder):
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80 shutil.rmtree(data_folder)
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81 else:
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82 os.remove(data_folder)
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83 except OSError as oserror:
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84 print "Cannot create data folder({0}): {1}".format(oserror.errno, oserror.strerror)
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85 shutil.copytree(self.out_path, data_folder)
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86 p = subprocess.Popen(['chmod', '-R', 'o+rx', '/var/www/html/JBrowse-1.12.1/jbrowse_hub'])
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yating-l
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87 p.communicate()
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88 shutil.rmtree(self.out_path)
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89
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90 #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
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91 #run it locally. May need modify
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92 def outHtml(self):
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93 with open(self.outfile, 'w') as htmlfile:
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94 htmlstr = 'The JBrowse Hub is created: <br>'
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95 zipfiles = '<li><a href = "%s">Download</a></li>'
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96 jbrowse_hub = '<li><a href = "http://192.168.56.11/JBrowse-1.12.1/index.html?data=jbrowse_hub/json" target="_blank">View JBrowse Hub</a></li>'
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97 filedir_abs = os.path.abspath(self.outfile)
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98 filedir = os.path.dirname(filedir_abs)
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99 filedir = os.path.join(filedir, self.outfolder)
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100 for root, dirs, files in os.walk(filedir):
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101 for file in files:
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102 if file.endswith('.zip'):
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103 relative_directory = os.path.relpath(root, filedir)
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104 relative_file_path = os.path.join(relative_directory, file)
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105 htmlstr += zipfiles % relative_file_path
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106 htmlstr += jbrowse_hub
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107 htmlfile.write(htmlstr)
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108
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109 def createTrackList(self):
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110 trackList = os.path.join(self.json, "trackList.json")
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111 if not os.path.exists(trackList):
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112 os.mknod(trackList)
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113
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114 def Bam(self, track, metadata):
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115 #create trackList.json if not exist
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116 self.createTrackList()
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117 json_file = os.path.join(self.json, "trackList.json")
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118 bam_track = dict()
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119 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
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120 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
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121 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
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122 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
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123 bam_track['label'] = metadata['label']
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124 bam_track['category'] = metadata['category']
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125 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
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126
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127 def BigWig(self, track, metadata):
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128 #create trackList.json if not exist
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129 self.createTrackList()
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130 json_file = os.path.join(self.json, "trackList.json")
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131 bigwig_track = dict()
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132 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
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133 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
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134 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
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135 bigwig_track['label'] = metadata['label']
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136 bigwig_track['style'] = metadata['style']
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137 bigwig_track['category'] = metadata['category']
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138 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
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139
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140 #If the metadata is not set, use the default value
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141 def SetMetadata(self, track, metadata):
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142 if 'label' not in metadata.keys() or metadata['label'] == '':
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143 metadata['label'] = track['fileName']
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144 if 'color' not in metadata.keys() or metadata['color'] == '':
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145 metadata['color'] = "#daa520"
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146 if track['dataType'] == 'bigwig':
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147 if 'style' not in metadata.keys():
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148 metadata['style'] = {}
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149 if 'pos_color' not in metadata['style'] or metadata['style']['pos_color'] == '':
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150 metadata['pos_color'] = "#FFA600"
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151 if 'neg_color' not in metadata['style'] or metadata['style']['neg_color'] == '':
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152 metadata['neg_color'] = "#005EFF"
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153 if 'category' not in metadata.keys() or metadata['category'] == '':
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154 metadata['category'] = "Default group"
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155 if track['dataType'] == 'blastxml':
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156 metadata['type'] = "G-OnRamp_plugin/BlastAlignment"
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157 elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna':
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158 metadata['type'] = "G-OnRamp_plugin/GenePred"
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159 else:
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160 metadata['type'] = "CanvasFeatures"
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161
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162
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163
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167