comparison jbrowse.py @ 10:1a6d882d340d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524

9:f422ba2e9aa5

    d = {t.tag: {} if t.attrib else None}
    children = list(t)
    if children:
        dd = defaultdict(list)
        for dc in map(etree_to_dict, children):
            for k, v in dc.iteritems():
                dd[k].append(v)
        d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.iteritems()}}
    if t.attrib:
        d[t.tag].update(('@' + k, v) for k, v in t.attrib.iteritems())
    if t.text:
        text = t.text.strip()
        if children or t.attrib:
            if text:
                d[t.tag]['#text'] = text

            os.path.join('data', 'trackList.json')
        ]
        self.subprocess_check_call(cmd)

    def _add_track_json(self, json_data):
        if len(json_data.keys()) == 0:
            return

        tmp = tempfile.NamedTemporaryFile(delete=False)
        tmp.write(json.dumps(json_data))
        tmp.close()

        cmd = [
            'perl', self._jbrowse_bin('flatfile-to-json.pl'),
            self.TN_TABLE.get(format, 'gff'),
            data,
            '--trackLabel', trackData['label'],
            # '--trackType', 'JBrowse/View/Track/CanvasFeatures',
            '--key', trackData['key']
        ]

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

            cmd += ['--type', gffOpts['match']]

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

        if 'trackType' in gffOpts:
            cmd += [
                '--trackType', gffOpts['trackType']
            ]
        else:
            cmd += [
                '--trackType', 'JBrowse/View/Track/CanvasFeatures'
            ]

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

        self.subprocess_check_call(cmd)

        for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']):
            log.info('Processing %s / %s', track['category'], track_human_label)
            outputTrackConfig['key'] = track_human_label
            hashData = [dataset_path, track_human_label, track['category']]
            outputTrackConfig['label'] = hashlib.md5('|'.join(hashData)).hexdigest() + '_%s' % i

            # Colour parsing is complex due to different track types having
            # different colour options.
            colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
            # This used to be done with a dict.update() call, however that wiped out any previous style settings...

        subprocess.check_call(cmd)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument('xml', type=file, help='Track Configuration')

    parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
    parser.add_argument('--outdir', help='Output directory', default='out')
    parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
    args = parser.parse_args()

10:1a6d882d340d

    d = {t.tag: {} if t.attrib else None}
    children = list(t)
    if children:
        dd = defaultdict(list)
        for dc in map(etree_to_dict, children):
            for k, v in dc.items():
                dd[k].append(v)
        d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
    if t.attrib:
        d[t.tag].update(('@' + k, v) for k, v in t.attrib.items())
    if t.text:
        text = t.text.strip()
        if children or t.attrib:
            if text:
                d[t.tag]['#text'] = text

            os.path.join('data', 'trackList.json')
        ]
        self.subprocess_check_call(cmd)

    def _add_track_json(self, json_data):
        if len(json_data) == 0:
            return

        tmp = tempfile.NamedTemporaryFile(delete=False)
        tmp.write(json.dumps(json_data))
        tmp.close()

        cmd = [
            'perl', self._jbrowse_bin('flatfile-to-json.pl'),
            self.TN_TABLE.get(format, 'gff'),
            data,
            '--trackLabel', trackData['label'],
            '--key', trackData['key']
        ]

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

            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']

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

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

        self.subprocess_check_call(cmd)

        for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']):
            log.info('Processing %s / %s', track['category'], track_human_label)
            outputTrackConfig['key'] = track_human_label
            hashData = [dataset_path, track_human_label, track['category']]
            outputTrackConfig['label'] = hashlib.md5('|'.join(hashData).encode('utf-8')).hexdigest() + '_%s' % i

            # Colour parsing is complex due to different track types having
            # different colour options.
            colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
            # This used to be done with a dict.update() call, however that wiped out any previous style settings...

        subprocess.check_call(cmd)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration')

    parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
    parser.add_argument('--outdir', help='Output directory', default='out')
    parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
    args = parser.parse_args()