def test_simple_search(self):
"""ESearch Access via a query should return accessions"""
s = ESearch(db='protein', rettype='gi', retmax=1000,
term='h**o[organism] AND myh7')
result = s.read()
parsed = ESearchResultParser(result)
assert '83304912' in parsed.IdList #gi of human cardiac beta myh7
def test_simple_search(self):
"""ESearch Access via a query should return accessions"""
s = ESearch(db='protein',
rettype='gi',
retmax=1000,
term='h**o[organism] AND myh7')
result = s.read()
parsed = ESearchResultParser(result)
assert '83304912' in parsed.IdList #gi of human cardiac beta myh7
def esearch(query, retmax, binsize=10000):
"""Wraps ESearch call"""
ids = set([])
bins = (retmax / binsize) + 1 # handle remainder, just overshoot it
for i in range(bins):
handle = ESearch(term=query, db='nucleotide', retmax=binsize,
retstart=binsize * i)
ids.update(parse_esearch(handle.read()))
return ids
