comparison jbrowse.py @ 33:0ae74c70b267 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"

32:6b774e9d6387

class JbrowseConnector(object):

    def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
        self.TN_TABLE = {
            'gff3': '--gff',
            'gff': '--gff',
            'bed': '--bed',
            'genbank': '--gbk',
        }

        self.cs = ColorScaling()
        self.jbrowse = jbrowse
        self.outdir = outdir
        self.genome_paths = genomes
        self.standalone = standalone

        })

        with open(trackList, 'w') as handle:
            json.dump(trackListData, handle, indent=2)

    def subprocess_check_call(self, command):
        log.debug('cd %s && %s', self.outdir, ' '.join(command))
        subprocess.check_call(command, cwd=self.outdir)

    def subprocess_popen(self, command):
        log.debug('cd %s && %s', self.outdir, command)
        p = subprocess.Popen(command, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
        output, err = p.communicate()

        trackData['scale'] = wiggleOpts['scale']

        self._add_track_json(trackData)

    def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
        dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
        cmd = ['ln', '-s', os.path.realpath(data), dest]
        self.subprocess_check_call(cmd)

            "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
        })
        self._add_track_json(trackData)

    def _sort_gff(self, data, dest):

        if not os.path.exists(dest):
            # Only index if not already done
            cmd = "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" % (data, dest)
            self.subprocess_popen(cmd)

            cmd = ['bgzip', '-f', dest]
            self.subprocess_popen(' '.join(cmd))
            cmd = ['tabix', '-f', '-p', 'gff', dest + '.gz']
            self.subprocess_popen(' '.join(cmd))

    def add_features(self, data, format, trackData, gffOpts, **kwargs):

        dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')

        self._sort_gff(data, dest)

        url = os.path.join('raw', trackData['label'] + '.gff.gz')

        elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
            if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
                trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']

        self._add_track_json(trackData)

        if gffOpts.get('index', 'false') == 'true':
            self.tracksToIndex.append("%s" % trackData['label'])

    def add_rest(self, url, trackData):

            if customTrackConfig:
                self.set_custom_track_options(customTrackConfig, outputTrackConfig, mapped_chars)

            # import pprint; pprint.pprint(track)
            # import sys; sys.exit()
            if dataset_ext in ('gff', 'gff3', 'bed'):
                self.add_features(dataset_path, dataset_ext, outputTrackConfig,
                                  track['conf']['options']['gff'])
            elif dataset_ext == 'bigwig':
                self.add_bigwig(dataset_path, outputTrackConfig,
                                track['conf']['options']['wiggle'])
            elif dataset_ext == 'bigwig_multiple':
                self.add_bigwig_multiple(dataset_path, outputTrackConfig,
                                         track['conf']['options']['wiggle'])
            elif dataset_ext == 'bam':
                real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
                if not isinstance(real_indexes, list):
                    # <bam_indices>
                    #  <bam_index>/path/to/a.bam.bai</bam_index>

33:0ae74c70b267

class JbrowseConnector(object):

    def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
        self.cs = ColorScaling()
        self.jbrowse = jbrowse
        self.outdir = outdir
        self.genome_paths = genomes
        self.standalone = standalone

        })

        with open(trackList, 'w') as handle:
            json.dump(trackListData, handle, indent=2)

    def subprocess_check_call(self, command, output=None):
        if output:
            log.debug('cd %s && %s >  %s', self.outdir, ' '.join(command), output)
            subprocess.check_call(command, cwd=self.outdir, stdout=output)
        else:
            log.debug('cd %s && %s', self.outdir, ' '.join(command))
            subprocess.check_call(command, cwd=self.outdir)

    def subprocess_popen(self, command):
        log.debug('cd %s && %s', self.outdir, command)
        p = subprocess.Popen(command, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
        output, err = p.communicate()

        trackData['scale'] = wiggleOpts['scale']

        self._add_track_json(trackData)

    def add_maf(self, data, trackData, mafOpts, **kwargs):
        script = os.path.realpath(os.path.join(self.jbrowse, 'plugins', 'MAFViewer', 'bin', 'maf2bed.pl'))
        dest = os.path.join('data', 'raw', trackData['label'] + '.txt')

        tmp1 = tempfile.NamedTemporaryFile(delete=False)
        tmp1.close()

        # Process MAF to bed-like
        cmd = [script, data]
        self.subprocess_check_call(cmd, output=tmp1.path)

        # Sort / Index it
        self._sort_bed(tmp1.path, dest)
        # Cleanup
        try:
            os.remove(tmp1.path)
        except OSError:
            pass

        # Construct samples list
        # We could get this from galaxy metadata, not sure how easily.
        ps = subprocess.Popen(['grep', '^s [^ ]*', '-o', data], stdout=subprocess.PIPE)
        output = subprocess.check_output(('sort', '-u'), stdin=ps.stdout)
        ps.wait()
        samples = [x[2:] for x in output]

        trackData.update({
            "storeClass": "MAFViewer/Store/SeqFeature/MAFTabix",
            "type": "MAFViewer/View/Track/MAF",
            "urlTemplate": trackData['label'] + '.txt.gz',
            "samples": samples,
        })

        self._add_track_json(trackData)

    def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
        dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
        cmd = ['ln', '-s', os.path.realpath(data), dest]
        self.subprocess_check_call(cmd)

            "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
        })
        self._add_track_json(trackData)

    def _sort_gff(self, data, dest):
        # Only index if not already done
        if not os.path.exists(dest):
            cmd = "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" % (data, dest)
            self.subprocess_popen(cmd)

            self.subprocess_check_call(['bgzip', '-f', dest])
            self.subprocess_check_call(['tabix', '-f', '-p', 'gff', dest + '.gz'])

    def _sort_bed(self, data, dest):
        # Only index if not already done
        if not os.path.exists(dest):
            cmd = ['sort', '-k1,1', '-k2,2n', data]
            self.subprocess_check_call(cmd, output=dest)

            self.subprocess_check_call(['bgzip', '-f', dest])
            self.subprocess_check_call(['tabix', '-f', '-p', 'bed', dest + '.gz'])

    def add_gff(self, data, format, trackData, gffOpts, **kwargs):
        dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')

        self._sort_gff(data, dest)

        url = os.path.join('raw', trackData['label'] + '.gff.gz')

        elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
            if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
                trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']

        self._add_track_json(trackData)

        if gffOpts.get('index', 'false') == 'true':
            self.tracksToIndex.append("%s" % trackData['label'])

    def add_bed(self, data, format, trackData, gffOpts, **kwargs):
        dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.bed')

        self._sort_bed(data, dest)

        url = os.path.join('raw', trackData['label'] + '.bed.gz')
        trackData.update({
            "urlTemplate": url,
            "storeClass": "JBrowse/Store/SeqFeature/BEDTabix",
        })

        if 'match' in gffOpts:
            trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'

        trackType = gffOpts.get('trackType', 'JBrowse/View/Track/CanvasFeatures')
        trackData['type'] = trackType

        if trackType in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
            if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
                trackData['transcriptType'] = gffOpts['transcriptType']
            if 'subParts' in gffOpts and gffOpts['subParts']:
                trackData['subParts'] = gffOpts['subParts']
            if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
                trackData['impliedUTRs'] = gffOpts['impliedUTRs']
        elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
            if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
                trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']

        self._add_track_json(trackData)

        if gffOpts.get('index', 'false') == 'true':
            self.tracksToIndex.append("%s" % trackData['label'])

    def add_genbank(self, data, format, trackData, gffOpts, **kwargs):
        cmd = [
            'perl', self._jbrowse_bin('flatfile-to-json.pl'),
            '--genbank', data,
            '--trackLabel', trackData['label'],
            '--key', trackData['key']
        ]

        # className in --clientConfig is ignored, it needs to be set with --className
        if 'className' in trackData['style']:
            cmd += ['--className', trackData['style']['className']]

        config = copy.copy(trackData)
        clientConfig = trackData['style']
        del config['style']

        if 'match' in gffOpts:
            config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
            if bool(gffOpts['match']):
                # Can be empty for CanvasFeatures = will take all by default
                cmd += ['--type', gffOpts['match']]

        cmd += ['--clientConfig', json.dumps(clientConfig)]

        trackType = 'JBrowse/View/Track/CanvasFeatures'
        if 'trackType' in gffOpts:
            trackType = gffOpts['trackType']

        if trackType == 'JBrowse/View/Track/CanvasFeatures':
            if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
                config['transcriptType'] = gffOpts['transcriptType']
            if 'subParts' in gffOpts and gffOpts['subParts']:
                config['subParts'] = gffOpts['subParts']
            if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
                config['impliedUTRs'] = gffOpts['impliedUTRs']
        elif trackType == 'JBrowse/View/Track/HTMLFeatures':
            if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
                cmd += ['--type', gffOpts['transcriptType']]

        cmd += [
            '--trackType', gffOpts['trackType']
        ]

        cmd.extend(['--config', json.dumps(config)])

        self.subprocess_check_call(cmd)

        if gffOpts.get('index', 'false') == 'true':
            self.tracksToIndex.append("%s" % trackData['label'])

    def add_rest(self, url, trackData):

            if customTrackConfig:
                self.set_custom_track_options(customTrackConfig, outputTrackConfig, mapped_chars)

            # import pprint; pprint.pprint(track)
            # import sys; sys.exit()
            if dataset_ext in ('gff', 'gff3'):
                self.add_gff(dataset_path, dataset_ext, outputTrackConfig,
                             track['conf']['options']['gff'])
            elif dataset_ext in ('bed', ):
                self.add_bed(dataset_path, dataset_ext, outputTrackConfig,
                             track['conf']['options']['gff'])
            elif dataset_ext in ('genbank', ):
                self.add_genbank(dataset_path, dataset_ext, outputTrackConfig,
                                 track['conf']['options']['gff'])
            elif dataset_ext == 'bigwig':
                self.add_bigwig(dataset_path, outputTrackConfig,
                                track['conf']['options']['wiggle'])
            elif dataset_ext == 'bigwig_multiple':
                self.add_bigwig_multiple(dataset_path, outputTrackConfig,
                                         track['conf']['options']['wiggle'])
            elif dataset_ext == 'maf':
                self.add_maf(dataset_path, outputTrackConfig,
                             track['conf']['options']['maf'])
            elif dataset_ext == 'bam':
                real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
                if not isinstance(real_indexes, list):
                    # <bam_indices>
                    #  <bam_index>/path/to/a.bam.bai</bam_index>