Mercurial > repos > yating-l > jbrowse_hub
comparison TrackHub.py @ 42:a5108e5010b4 draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
| author | yating-l |
|---|---|
| date | Mon, 20 Mar 2017 12:35:33 -0400 |
| parents | 75edbc203532 |
| children | 37422f705e9b |
comparison
equal
deleted
inserted
replaced
| 41:6a5f78bc0bed | 42:a5108e5010b4 |
|---|---|
| 5 import shutil | 5 import shutil |
| 6 import utils | 6 import utils |
| 7 | 7 |
| 8 | 8 |
| 9 class TrackHub: | 9 class TrackHub: |
| 10 def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path): | 10 def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData): |
| 11 self.input_files = inputFiles.tracks | 11 self.input_files = inputFiles.tracks |
| 12 self.outfile = outputDirect | 12 self.outfile = outputDirect |
| 13 self.outfolder = extra_files_path | 13 self.outfolder = extra_files_path |
| 14 self.out_path = os.path.join(extra_files_path, genome) | 14 self.out_path = os.path.join(extra_files_path, genome) |
| 15 self.reference = reference | 15 self.reference = reference |
| 16 self.tool_dir = tool_dir | 16 self.tool_dir = tool_dir |
| 17 self.metaData = metaData | |
| 17 self.raw = os.path.join(self.out_path, 'raw') | 18 self.raw = os.path.join(self.out_path, 'raw') |
| 18 self.json = os.path.join(self.out_path, 'json') | 19 self.json = os.path.join(self.out_path, 'json') |
| 19 try: | 20 try: |
| 20 if os.path.exists(self.json): | 21 if os.path.exists(self.json): |
| 21 shutil.rmtree(self.json) | 22 shutil.rmtree(self.json) |
| 42 p.communicate() | 43 p.communicate() |
| 43 except OSError as e: | 44 except OSError as e: |
| 44 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror) | 45 print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror) |
| 45 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings | 46 #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings |
| 46 def addTrack(self, track): | 47 def addTrack(self, track): |
| 47 track_label = track['label'] | 48 print "false_path" , track['false_path'] |
| 48 track_color = track['track_color'] | 49 if track['false_path'] in self.metaData.keys(): |
| 49 if track['dataType'] == 'blastxml': | 50 metadata = self.metaData[track['false_path']] |
| 50 track_type = "G-OnRamp_plugin/BlastAlignment" | |
| 51 elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna': | |
| 52 track_type = "G-OnRamp_plugin/GenePred" | |
| 53 else: | 51 else: |
| 54 track_type = "CanvasFeatures" | 52 metadata = {} |
| 53 self.SetMetadata(track, metadata) | |
| 55 if track['dataType'] == 'bam': | 54 if track['dataType'] == 'bam': |
| 56 self.createTrackList() | 55 self.Bam(track, metadata) |
| 57 json_file = os.path.join(self.json, "trackList.json") | |
| 58 bam_track = dict() | |
| 59 bam_track['type'] = 'JBrowse/View/Track/Alignments2' | |
| 60 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM' | |
| 61 bam_track['label'] = track_label | |
| 62 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName']) | |
| 63 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index']) | |
| 64 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') | |
| 65 # print "add bam track\n" | 56 # print "add bam track\n" |
| 66 elif track['dataType'] == 'bigwig': | 57 elif track['dataType'] == 'bigwig': |
| 67 self.createTrackList() | 58 self.BigWig(track, metadata) |
| 68 json_file = os.path.join(self.json, "trackList.json") | |
| 69 bigwig_track = dict() | |
| 70 bigwig_track['label'] = track_label | |
| 71 #color_setting = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']} | |
| 72 bigwig_track['style'] = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']} | |
| 73 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName']) | |
| 74 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' | |
| 75 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig' | |
| 76 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks') | |
| 77 else: | 59 else: |
| 78 gff3_file = os.path.join(self.raw, track['fileName']) | 60 gff3_file = os.path.join(self.raw, track['fileName']) |
| 79 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf': | 61 if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf': |
| 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]) | 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]) |
| 81 elif track['dataType'] == 'gff3_transcript': | 63 elif track['dataType'] == 'gff3_transcript': |
| 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]) | 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]) |
| 83 else: | 65 else: |
| 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]) | 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]) |
| 85 p.communicate() | 67 p.communicate() |
| 86 | 68 |
| 87 def indexName(self): | 69 def indexName(self): |
| 88 p = subprocess.Popen(['generate-names.pl', '-v', '--out', self.json]) | 70 p = subprocess.Popen(['generate-names.pl', '-v', '--out', self.json]) |
| 89 p.communicate() | 71 p.communicate() |
| 113 | 95 |
| 114 def createTrackList(self): | 96 def createTrackList(self): |
| 115 trackList = os.path.join(self.json, "trackList.json") | 97 trackList = os.path.join(self.json, "trackList.json") |
| 116 if not os.path.exists(trackList): | 98 if not os.path.exists(trackList): |
| 117 os.mknod(trackList) | 99 os.mknod(trackList) |
| 100 | |
| 101 def Bam(self, track, metadata): | |
| 102 #create trackList.json if not exist | |
| 103 self.createTrackList() | |
| 104 json_file = os.path.join(self.json, "trackList.json") | |
| 105 bam_track = dict() | |
| 106 bam_track['type'] = 'JBrowse/View/Track/Alignments2' | |
| 107 bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM' | |
| 108 bam_track['urlTemplate'] = os.path.join('../raw', track['fileName']) | |
| 109 bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index']) | |
| 110 bam_track.update(metadata) | |
| 111 utils.add_tracks_to_json(json_file, bam_track, 'add_tracks') | |
| 112 | |
| 113 def BigWig(self, track, metadata): | |
| 114 #create trackList.json if not exist | |
| 115 self.createTrackList() | |
| 116 json_file = os.path.join(self.json, "trackList.json") | |
| 117 bigwig_track = dict() | |
| 118 #color_setting = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']} | |
| 119 #bigwig_track['style'] = {"pos_color" : track['pos_color'], "neg_color" : track['neg_color']} | |
| 120 bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName']) | |
| 121 bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot' | |
| 122 bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig' | |
| 123 bigwig_track.update(metadata) | |
| 124 utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks') | |
| 125 | |
| 126 #If the metadata is not set, use the default value | |
| 127 def SetMetadata(self, track, metadata): | |
| 128 print metadata | |
| 129 #track.update(metadata) | |
| 130 if 'label' not in metadata.keys() or metadata['label'] == '': | |
| 131 metadata['label'] = track['fileName'] | |
| 132 if 'color' not in metadata.keys() or metadata['color'] == '': | |
| 133 metadata['color'] = "#daa520" | |
| 134 if track['dataType'] == 'bigwig': | |
| 135 if 'style' not in metadata.keys(): | |
| 136 metadata['style'] = {} | |
| 137 if 'pos_color' not in metadata['style'] or metadata['style']['pos_color'] == '': | |
| 138 metadata['pos_color'] = "#FFA600" | |
| 139 if 'neg_color' not in metadata['style'] or metadata['style']['neg_color'] == '': | |
| 140 metadata['neg_color'] = "#005EFF" | |
| 141 if 'category' not in metadata.keys() or metadata['category'] == '': | |
| 142 metadata['category'] = "Default group" | |
| 143 if track['dataType'] == 'blastxml': | |
| 144 metadata['type'] = "G-OnRamp_plugin/BlastAlignment" | |
| 145 elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna': | |
| 146 metadata['type'] = "G-OnRamp_plugin/GenePred" | |
| 147 else: | |
| 148 metadata['type'] = "CanvasFeatures" | |
| 149 | |
| 118 | 150 |
| 119 | 151 |
| 120 | 152 |
| 121 | 153 |
| 122 | 154 |