def test_find_repetitive_in_range():
pos = 0
neg = 0
# some should be positive, others negative
for txid in known_juncs:
expected = txid in cross_hash_seqs
if expected == True:
pos += 1
else:
neg += 1
my_query_juncs = query_juncs.get(txid,[])
for query_junc in my_query_juncs:
minus_range, plus_range = find_match_range(query_junc,seqs,20)
yield check_find_repetitive_in_range, query_junc, minus_range, plus_range, expected
# all negative
for txid in unmatched_query_juncs:
my_query_juncs = unmatched_query_juncs.get(txid,[])
for query_junc in my_query_juncs:
minus_range, plus_range = find_match_range(query_junc,seqs,20)
yield check_find_repetitive_in_range, query_junc, minus_range, plus_range, False
# make sure we found a bunch of each type
assert_greater(pos,0)
assert_greater(neg,0)
def test_find_repetitive_in_range():
pos = 0
neg = 0
# some should be positive, others negative
for txid in known_juncs:
expected = txid in cross_hash_seqs
if expected == True:
pos += 1
else:
neg += 1
my_query_juncs = query_juncs.get(txid, [])
for query_junc in my_query_juncs:
minus_range, plus_range = find_match_range(query_junc, seqs, 20)
yield check_find_repetitive_in_range, query_junc, minus_range, plus_range, expected
# all negative
for txid in unmatched_query_juncs:
my_query_juncs = unmatched_query_juncs.get(txid, [])
for query_junc in my_query_juncs:
minus_range, plus_range = find_match_range(query_junc, seqs, 20)
yield check_find_repetitive_in_range, query_junc, minus_range, plus_range, False
# make sure we found a bunch of each type
assert_greater(pos, 0)
assert_greater(neg, 0)
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_match_range(txid,max_slide):
"""Check output of :py:func:`find_match_range` against known data
Parameters
----------
txid : str
ID of transcript to check
"""
my_juncs = known_juncs.get(txid,[])
for n,my_junc in enumerate(my_juncs):
ref_minus, ref_plus = match_ranges[txid][n]
ref_minus = max(-max_slide, ref_minus)
ref_plus = min(max_slide+1, ref_plus)
found_minus, found_plus = find_match_range(my_junc,seqs,max_slide)
assert_equal(ref_minus,found_minus,"Minus match ranges don't match. Expected %s, got %s" % (ref_minus,found_minus))
assert_equal(ref_plus,found_plus, "Plus match ranges don't match. Expected %s, got %s" % (ref_plus,found_plus))
def check_find_match_range(txid, max_slide):
"""Check output of :py:func:`find_match_range` against known data
Parameters
----------
txid : str
ID of transcript to check
"""
my_juncs = known_juncs.get(txid, [])
for n, my_junc in enumerate(my_juncs):
ref_minus, ref_plus = match_ranges[txid][n]
ref_minus = max(-max_slide, ref_minus)
ref_plus = min(max_slide + 1, ref_plus)
found_minus, found_plus = find_match_range(my_junc, seqs, max_slide)
assert_equal(
ref_minus, found_minus,
"Minus match ranges don't match. Expected %s, got %s" %
(ref_minus, found_minus))
assert_equal(
ref_plus, found_plus,
"Plus match ranges don't match. Expected %s, got %s" %
(ref_plus, found_plus))
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_known_in_range(query_junc):
minus_range, plus_range = find_match_range(query_junc, seqs, 20)
found_known = find_known_in_range(query_junc, minus_range, plus_range,
all_known_juncs)
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([]))
def check_find_none_when_none_known_in_range(query_junc):
minus_range, plus_range = find_match_range(query_junc,seqs,20)
found_known = find_known_in_range(query_junc,minus_range,plus_range,all_known_juncs)
found_known = set([str(X) for X in found_known])
assert_set_equal(found_known,set([]))
