Mercurial > repos > iuc > jbrowse
comparison jbrowse.py @ 12:db5fe5a3176a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
| author | iuc |
|---|---|
| date | Mon, 06 Feb 2017 12:52:09 -0500 |
| parents | 4cbceec1d6b4 |
| children | 69c5e9c0add0 |
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| 11:4cbceec1d6b4 | 12:db5fe5a3176a |
|---|---|
| 156 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)] | 156 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)] |
| 157 self.brewer_colour_idx += 1 | 157 self.brewer_colour_idx += 1 |
| 158 return r, g, b | 158 return r, g, b |
| 159 | 159 |
| 160 def parse_menus(self, track): | 160 def parse_menus(self, track): |
| 161 trackConfig = {'menuTemplate': [{}, {}, {}]} | 161 trackConfig = {'menuTemplate': [{}, {}, {}, {}]} |
| 162 | 162 |
| 163 if 'menu' in track['menus']: | 163 if 'menu' in track['menus']: |
| 164 menu_list = [track['menus']['menu']] | 164 menu_list = [track['menus']['menu']] |
| 165 if isinstance(track['menus']['menu'], list): | 165 if isinstance(track['menus']['menu'], list): |
| 166 menu_list = track['menus']['menu'] | 166 menu_list = track['menus']['menu'] |
| 433 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): | 433 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): |
| 434 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') | 434 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') |
| 435 cmd = ['ln', data, dest] | 435 cmd = ['ln', data, dest] |
| 436 self.subprocess_check_call(cmd) | 436 self.subprocess_check_call(cmd) |
| 437 | 437 |
| 438 url = os.path.join('raw', trackData['label'] + '.bw') | |
| 438 trackData.update({ | 439 trackData.update({ |
| 439 "urlTemplate": os.path.join('..', dest), | 440 "urlTemplate": url, |
| 440 "storeClass": "JBrowse/Store/SeqFeature/BigWig", | 441 "storeClass": "JBrowse/Store/SeqFeature/BigWig", |
| 441 "type": "JBrowse/View/Track/Wiggle/Density", | 442 "type": "JBrowse/View/Track/Wiggle/Density", |
| 442 }) | 443 }) |
| 443 | 444 |
| 444 trackData['type'] = wiggleOpts['type'] | 445 trackData['type'] = wiggleOpts['type'] |
| 458 self.subprocess_check_call(cmd) | 459 self.subprocess_check_call(cmd) |
| 459 | 460 |
| 460 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai'] | 461 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai'] |
| 461 self.subprocess_check_call(cmd) | 462 self.subprocess_check_call(cmd) |
| 462 | 463 |
| 464 url = os.path.join('raw', trackData['label'] + '.bam') | |
| 463 trackData.update({ | 465 trackData.update({ |
| 464 "urlTemplate": os.path.join('..', dest), | 466 "urlTemplate": url, |
| 465 "type": "JBrowse/View/Track/Alignments2", | 467 "type": "JBrowse/View/Track/Alignments2", |
| 466 "storeClass": "JBrowse/Store/SeqFeature/BAM", | 468 "storeClass": "JBrowse/Store/SeqFeature/BAM", |
| 467 }) | 469 }) |
| 468 | 470 |
| 469 self._add_track_json(trackData) | 471 self._add_track_json(trackData) |
| 485 cmd = ['bgzip', dest] | 487 cmd = ['bgzip', dest] |
| 486 self.subprocess_check_call(cmd) | 488 self.subprocess_check_call(cmd) |
| 487 cmd = ['tabix', '-p', 'vcf', dest + '.gz'] | 489 cmd = ['tabix', '-p', 'vcf', dest + '.gz'] |
| 488 self.subprocess_check_call(cmd) | 490 self.subprocess_check_call(cmd) |
| 489 | 491 |
| 492 url = os.path.join('raw', trackData['label'] + '.vcf') | |
| 490 trackData.update({ | 493 trackData.update({ |
| 491 "urlTemplate": os.path.join('..', dest + '.gz'), | 494 "urlTemplate": url, |
| 492 "type": "JBrowse/View/Track/HTMLVariants", | 495 "type": "JBrowse/View/Track/HTMLVariants", |
| 493 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", | 496 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", |
| 494 }) | 497 }) |
| 495 self._add_track_json(trackData) | 498 self._add_track_json(trackData) |
| 496 | 499 |
| 562 for subkey in colourOptions['style']: | 565 for subkey in colourOptions['style']: |
| 563 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey] | 566 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey] |
| 564 else: | 567 else: |
| 565 outputTrackConfig[key] = colourOptions[key] | 568 outputTrackConfig[key] = colourOptions[key] |
| 566 | 569 |
| 567 menus = self.cs.parse_menus(track['conf']['options']) | 570 if 'menus' in track['conf']['options']: |
| 568 outputTrackConfig.update(menus) | 571 menus = self.cs.parse_menus(track['conf']['options']) |
| 572 outputTrackConfig.update(menus) | |
| 569 | 573 |
| 570 # import pprint; pprint.pprint(track) | 574 # import pprint; pprint.pprint(track) |
| 571 # import sys; sys.exit() | 575 # import sys; sys.exit() |
| 572 if dataset_ext in ('gff', 'gff3', 'bed'): | 576 if dataset_ext in ('gff', 'gff3', 'bed'): |
| 573 self.add_features(dataset_path, dataset_ext, outputTrackConfig, | 577 self.add_features(dataset_path, dataset_ext, outputTrackConfig, |