def __init__(self, corpusdir, **kwargs):
self.mirbase = MirbaseDB(config.mirbase_path)
self.mirbase.load_graph()
self.mirnas = {}
self.tfs = {}
self.pairs = {}
self.pmids = set()
self.normalized_mirnas = set() # normalized to miRBase
self.normalized_tfs = set() #normalized to maybe UniProt
self.normalized_pairs = set()
self.db_path = corpusdir
self.load_database()
super(TransmirCorpus, self).__init__(corpusdir, self.pmids, **kwargs)
mirna_stopwords = set([
"mediated", "expressing", "deficient", "transfected", "dependent",
"family", "specific", "null", "independent", "dependant", "overexpressing",
"binding", "targets", "induced"
])
# "mirna", "mirnas", "mir", "hsa-mir"])
mirna_nextstopwords = set(["inhibitor"])
with open(config.stoplist, 'r') as stopfile:
for l in stopfile:
w = l.strip().lower()
if w not in mirna_stopwords and len(w) > 1:
mirna_stopwords.add(w)
mirna_stopwords.discard("let")
mirna_graph = MirbaseDB(config.mirbase_path)
mirna_graph.load_graph()
class MirnaEntity(Entity):
def __init__(self, tokens, sid, *args, **kwargs):
# Entity.__init__(self, kwargs)
super(MirnaEntity, self).__init__(tokens, **kwargs)
self.type = "mirna"
self.subtype = kwargs.get("subtype")
self.mirna_acc = None
self.mirna_name = 0
self.sid = sid
self.nextword = kwargs.get("nextword")
self.go_ids = []
