Mercurial > repos > yating-l > jbrowsearchivecreator

annotate TrackHub.py @ 10:91b3558fa73f draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 479fc6490e24ca0e5034ae6c3579882e97e095e6-dirty
author yating-l
date Wed, 31 May 2017 13:38:46 -0400
parents 8d1cf7ce65cd
children 45b5cb50c29e
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yating-l
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1 #!/usr/bin/env python
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2
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3 import os
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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4 import subprocess
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5 import shutil
10
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6 import zipfile
0
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7 import json
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8 import utils
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9
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10
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11 class TrackHub:
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12 def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData, jbrowse_host):
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13 self.input_files = inputFiles.tracks
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14 self.outfile = outputDirect
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15 self.outfolder = extra_files_path
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16 self.out_path = os.path.join(extra_files_path, genome)
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17 self.reference = reference
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18 self.tool_dir = tool_dir
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19 self.metaData = metaData
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20 self.raw = os.path.join(self.out_path, 'raw')
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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21 self.json = os.path.join(self.out_path, 'json')
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22 self.jbrowse_host = jbrowse_host
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23 try:
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24 if os.path.exists(self.json):
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25 shutil.rmtree(self.json)
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26 os.makedirs(self.json)
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27 except OSError as e:
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28 print "Cannot create json folder error({0}): {1}".format(e.errno, e.strerror)
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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29 else:
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30 print "Create jbrowse folder {}".format(self.out_path)
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31
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32 def createHub(self):
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33 self.prepareRefseq()
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34 for input_file in self.input_files:
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35 self.addTrack(input_file)
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36 self.indexName()
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37 slink = self.makeArchive()
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38 self.outHtml(slink)
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39 print "Success!\n"
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40
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41 def prepareRefseq(self):
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42 try:
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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43 #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
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44 subprocess.call(['prepare-refseqs.pl', '--fasta', self.reference, '--out', self.json])
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45 except OSError as e:
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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46 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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47 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
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48 def addTrack(self, track):
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49 #print "false_path" , track['false_path']
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50 if track['false_path'] in self.metaData.keys():
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51 metadata = self.metaData[track['false_path']]
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52 else:
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53 metadata = {}
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54 self.SetMetadata(track, metadata)
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55 if track['dataType'] == 'bam':
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56 self.Bam(track, metadata)
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57 # print "add bam track\n"
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58 elif track['dataType'] == 'bigwig':
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59 self.BigWig(track, metadata)
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60 else:
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61 flat_file = os.path.join(self.raw, track['fileName'])
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62 if track['dataType'] == 'bed':
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63 subprocess.call(['flatfile-to-json.pl', '--bed', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
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64 elif track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf' or track['dataType'] == 'blastxml':
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65 subprocess.call(['flatfile-to-json.pl', '--gff', flat_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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66 elif track['dataType'] == 'gff3_transcript':
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67 subprocess.call(['flatfile-to-json.pl', '--gff', flat_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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68 else:
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69 subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
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70
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71 def indexName(self):
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72 subprocess.call(['generate-names.pl', '-v', '--out', self.json])
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73 print "finished name index \n"
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74
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75 def makeArchive(self):
10
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76 #shutil.make_archive(self.out_path, 'zip', self.out_path)
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77 os.chdir(os.path.dirname(self.out_path))
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78 with zipfile.ZipFile(self.out_path + '.zip', 'w', zipfile.ZIP_DEFLATED, allowZip64=True) as zf:
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79 for root, _, filenames in os.walk(os.path.basename(self.out_path)):
91b3558fa73f planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 479fc6490e24ca0e5034ae6c3579882e97e095e6-dirty
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80 for name in filenames:
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81 name = os.path.join(root, name)
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82 name = os.path.normpath(name)
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83 zf.write(name, name)
0
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84 file_dir = os.path.abspath(self.outfile)
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85 source_dir = os.path.dirname(file_dir)
8d1cf7ce65cd planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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86 folder_name = os.path.basename(self.outfolder)
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87 source_name = os.path.basename(self.out_path)
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88 source = os.path.join(source_dir, folder_name, source_name)
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89 slink = source.replace('/', '_')
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diff changeset
90 slink = os.path.join('/var/www/html/JBrowse-1.12.1/data', slink)
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diff changeset
91 try:
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92 if os.path.islink(slink):
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93 os.unlink(slink)
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94 except OSError as oserror:
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95 print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror)
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96 os.symlink(source, slink)
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97 return slink
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98
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99 #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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100 #run it locally. May need modify
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101 def outHtml(self, slink):
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102 with open(self.outfile, 'w') as htmlfile:
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103 htmlstr = 'The JBrowse Hub is created: <br>'
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104 zipfiles = '<li><a href = "%s">Download</a></li>'
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105 url = self.jbrowse_host + "/JBrowse-1.12.1/index.html?data=%s"
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106 jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub</a></li>' % url
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107 filedir_abs = os.path.abspath(self.outfile)
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108 filedir = os.path.dirname(filedir_abs)
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109 filedir = os.path.join(filedir, self.outfolder)
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110 for root, dirs, files in os.walk(filedir):
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111 for file in files:
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112 if file.endswith('.zip'):
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113 relative_directory = os.path.relpath(root, filedir)
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114 relative_file_path = os.path.join(relative_directory, file)
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115 htmlstr += zipfiles % relative_file_path
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116 link_name = os.path.basename(slink)
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117 relative_path = os.path.join('data', link_name + '/json')
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118 htmlstr += jbrowse_hub % relative_path
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119 htmlfile.write(htmlstr)
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120
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121 def createTrackList(self):
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122 trackList = os.path.join(self.json, "trackList.json")
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123 if not os.path.exists(trackList):
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124 os.mknod(trackList)
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125
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126 def Bam(self, track, metadata):
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127 #create trackList.json if not exist
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128 self.createTrackList()
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129 json_file = os.path.join(self.json, "trackList.json")
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130 bam_track = dict()
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131 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
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132 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
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133 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
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134 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
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135 bam_track['label'] = metadata['label']
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136 bam_track['category'] = metadata['category']
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137 bam_track = json.dumps(bam_track)
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138 #Use add-track-json.pl to add bam track to json file
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139 new_track = subprocess.Popen(['echo', bam_track], stdout=subprocess.PIPE)
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140 subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
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141
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142 def BigWig(self, track, metadata):
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143 #create trackList.json if not exist
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144 self.createTrackList()
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145 json_file = os.path.join(self.json, "trackList.json")
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146 bigwig_track = dict()
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147 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
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148 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
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149 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
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150 bigwig_track['label'] = metadata['label']
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151 bigwig_track['style'] = metadata['style']
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152 bigwig_track['category'] = metadata['category']
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153 bigwig_track = json.dumps(bigwig_track)
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154 #Use add-track-json.pl to add bigwig track to json file
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155 new_track = subprocess.Popen(['echo', bigwig_track], stdout=subprocess.PIPE)
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156 #output = new_track.communicate()[0]
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157 subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
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158
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159 #If the metadata is not set, use the default value
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160 def SetMetadata(self, track, metadata):
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161 if 'label' not in metadata.keys() or metadata['label'] == '':
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162 metadata['label'] = track['fileName']
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163 if 'color' not in metadata.keys() or metadata['color'] == '':
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164 metadata['color'] = "#daa520"
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165 if track['dataType'] == 'bigwig':
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166 if 'style' not in metadata.keys():
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167 metadata['style'] = {}
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168 if 'pos_color' not in metadata['style'] or metadata['style']['pos_color'] == '':
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169 metadata['style']['pos_color'] = "#FFA600"
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170 if 'neg_color' not in metadata['style'] or metadata['style']['neg_color'] == '':
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171 metadata['style']['neg_color'] = "#005EFF"
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172 if 'category' not in metadata.keys() or metadata['category'] == '':
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173 metadata['category'] = "Default group"
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174 if track['dataType'] == 'blastxml':
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175 metadata['type'] = "G-OnRamp_plugin/BlastAlignment"
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176 elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna':
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177 metadata['type'] = "G-OnRamp_plugin/GenePred"
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178 else:
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179 metadata['type'] = "CanvasFeatures"
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180
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181
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182
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183
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184
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185
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186