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
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)]
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)]