Example #1
0
def get_ucsc_oreganno_track(url):
    "@return: Yield regions corresponding to the ORegAnno track in UCSC indexed by the URL."
    logging.info('Enumerating entry points to %s', url)
    entry_points = [id for id, start, stop, orientation in das.fetch_entry_points(url)]
    logging.info('Fetching ORegAnno features from %s', url)
    oreganno_segments = das.fetch_features(url, entry_points, types=('oreganno',))
    for segment in oreganno_segments:
        id_ = segment.get('id')
        for feature in segment.findall('FEATURE'):
            label = feature.get('label')
            start = int(feature.find('START').text)
            end = int(feature.find('END').text)
            orientation = feature.find('ORIENTATION').text
            yield label, id_, start, end, orientation
Example #2
0
 def __init__(self, prefix):
     "Prefix specifies a DAS prefix for genome of interest."
     self.prefix = prefix
     self.entry_points = [ep for ep in das.fetch_entry_points(prefix)]
Example #3
0
 def __init__(self, prefix):
     "Prefix specifies a DAS prefix for genome of interest."
     self.prefix = prefix
     self.entry_points = [ep for ep in das.fetch_entry_points(prefix)]