Mercurial > repos > yating-l > jbrowsearchivecreator

annotate TrackHub.py @ 0:8d1cf7ce65cd draft

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