Mercurial > repos > yating-l > jbrowse_hub

annotate TrackHub.py @ 40:4af741177682 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty
author yating-l
date Fri, 17 Mar 2017 19:01:21 -0400
parents 75edbc203532
children a5108e5010b4
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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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yating-l
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10 def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path):
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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.raw = os.path.join(self.out_path, 'raw')
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18 self.json = os.path.join(self.out_path, 'json')
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19 try:
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20 if os.path.exists(self.json):
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21 shutil.rmtree(self.json)
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22 os.makedirs(self.json)
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23 except OSError as e:
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24 print "Cannot create json folder error({0}): {1}".format(e.errno, e.strerror)
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25 else:
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26 print "Create jbrowse folder {}".format(self.out_path)
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28 def createHub(self):
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29 self.prepareRefseq()
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30 for input_file in self.input_files:
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31 self.addTrack(input_file)
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32 self.indexName()
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33 self.makeArchive()
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34 self.outHtml()
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35 print "Success!\n"
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37 def prepareRefseq(self):
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38 try:
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39 #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
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40 p = subprocess.Popen(['prepare-refseqs.pl', '--fasta', self.reference, '--out', self.json])
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41 # Wait for process to terminate.
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42 p.communicate()
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43 except OSError as e:
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44 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
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45 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
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46 def addTrack(self, track):
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47 track_label = track['label']
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48 track_color = track['track_color']
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49 if track['dataType'] == 'blastxml':
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50 track_type = "G-OnRamp_plugin/BlastAlignment"
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51 elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna':
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52 track_type = "G-OnRamp_plugin/GenePred"
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53 else:
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54 track_type = "CanvasFeatures"
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55 if track['dataType'] == 'bam':
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56 self.createTrackList()
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57 json_file = os.path.join(self.json, "trackList.json")
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58 bam_track = dict()
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59 bam_track['type'] = 'JBrowse/View/Track/Alignments2'
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60 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
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61 bam_track['label'] = track_label
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62 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
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63 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
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64 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
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65 # print "add bam track\n"
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66 elif track['dataType'] == 'bigwig':
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67 self.createTrackList()
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68 json_file = os.path.join(self.json, "trackList.json")
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69 bigwig_track = dict()
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70 bigwig_track['label'] = track_label
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71 #color_setting = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']}
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72 bigwig_track['style'] = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']}
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73 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
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74 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
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75 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
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76 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
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77 else:
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78 gff3_file = os.path.join(self.raw, track['fileName'])
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79 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf':
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80 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--Config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments"}', '--clientConfig', '{"color" : "%s"}' % track_color, '--out', self.json])
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81 elif track['dataType'] == 'gff3_transcript':
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82 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--Config', '{"transcriptType": "transcript"}', '--clientConfig', '{"color" : "%s"}' % track_color, '--out', self.json])
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83 else:
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84 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', track_type, '--trackLabel', track_label, '--clientConfig', '{"color" : "%s"}' % track_color, '--out', self.json])
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85 p.communicate()
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87 def indexName(self):
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88 p = subprocess.Popen(['generate-names.pl', '-v', '--out', self.json])
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89 p.communicate()
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90 print "finished name index \n"
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91
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92 def makeArchive(self):
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93 shutil.make_archive(self.out_path, 'zip', self.out_path)
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94 shutil.rmtree(self.out_path)
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95
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96 #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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97 #run it locally. May need modify
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98 def outHtml(self):
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99 with open(self.outfile, 'w') as htmlfile:
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100 htmlstr = 'The JBrowse Hub is created: <br>'
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101 zipfiles = '<li><a href = "%s">Download</a></li>'
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102 filedir_abs = os.path.abspath(self.outfile)
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103 filedir = os.path.dirname(filedir_abs)
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104 filedir = os.path.join(filedir, self.outfolder)
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105 for root, dirs, files in os.walk(filedir):
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106 for file in files:
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107 if file.endswith('.zip'):
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108 relative_directory = os.path.relpath(root, filedir)
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109 relative_file_path = os.path.join(relative_directory, file)
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110 htmlstr += zipfiles % relative_file_path
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111
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112 htmlfile.write(htmlstr)
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113
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114 def createTrackList(self):
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115 trackList = os.path.join(self.json, "trackList.json")
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116 if not os.path.exists(trackList):
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117 os.mknod(trackList)
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118
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119
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