def check_find_canonicals_in_range(query_junc):
txid = query_junc.chrom
minus_range, plus_range = find_match_range(query_junc,seqs,20)
found_can = find_canonicals_in_range(query_junc,minus_range,plus_range,seqs,canonicals[query_junc.strand])
found_can = set([str(X) for X in found_can])
expected = set([str(X) for X in known_juncs.get(txid,[])])
assert_set_equal(expected,found_can,("Known junction not found for %s. "+\
"Query: %s\n Expected %s\n " +\
"Got %s\n match range: (%s,%s)") % (txid,
str(query_junc),
expected,
found_can,
minus_range,
plus_range))
def check_find_canonicals_in_range(query_junc):
txid = query_junc.chrom
minus_range, plus_range = find_match_range(query_junc, seqs, 20)
found_can = find_canonicals_in_range(query_junc, minus_range, plus_range,
seqs, canonicals[query_junc.strand])
found_can = set([str(X) for X in found_can])
expected = set([str(X) for X in known_juncs.get(txid, [])])
assert_set_equal(expected,found_can,("Known junction not found for %s. "+\
"Query: %s\n Expected %s\n " +\
"Got %s\n match range: (%s,%s)") % (txid,
str(query_junc),
expected,
found_can,
minus_range,
plus_range))
def check_find_none_when_none_canonical_in_range(query_junc):
minus_range, plus_range = find_match_range(query_junc, seqs, 20)
found_known = find_canonicals_in_range(query_junc, minus_range, plus_range,
seqs, canonicals[query_junc.strand])
found_known = set([str(X) for X in found_known])
assert_set_equal(found_known, set([]))
def check_find_none_when_none_canonical_in_range(query_junc):
minus_range, plus_range = find_match_range(query_junc,seqs,20)
found_known = find_canonicals_in_range(query_junc,minus_range,plus_range,seqs,canonicals[query_junc.strand])
found_known = set([str(X) for X in found_known])
assert_set_equal(found_known,set([]))
