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Merged
mr-c merged 4 commits into from
Jul 22, 2014
Merged

Fix/444 #542

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838b1ea
Changed amount of memory needed for test_save_load_merge
Jul 22, 2014
9c3799e
Reduced memory requirements for test_counting_single.py
Jul 22, 2014
89e3137
Updated Changelog
Jul 22, 2014
b7cacdb
Modified test_counting_single.py to pass the tests.
Jul 22, 2014
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3 changes: 3 additions & 0 deletions ChangeLog
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Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
2014-07-22 Leonor Garcia-Gutierrez <l.garcia-gutierrez@warwick.ac.uk>
* reduced memory requirements in test_counting_single.py

2014-07-21 Titus Brown <t@idyll.org>

* sandbox/saturate-by-median.py: introduce new sandbox script for
Expand Down
44 changes: 22 additions & 22 deletions tests/test_counting_single.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@


def test_no_collision():
kh = khmer.new_hashtable(4, 86)
kh = khmer.new_hashtable(4, 4)

kh.count('AAAA')
assert kh.get('AAAA') == 1
Expand All @@ -25,7 +25,7 @@ def test_no_collision():


def test_collision():
kh = khmer.new_hashtable(4, 85)
kh = khmer.new_hashtable(4, 4)

kh.count('AAAA')
assert kh.get('AAAA') == 1
Expand All @@ -35,7 +35,7 @@ def test_collision():


def test_badcount():
countingtable = khmer.new_hashtable(4, 85)
countingtable = khmer.new_hashtable(4, 4)
try:
countingtable.count()
assert 0, "count should require one argument"
Expand All @@ -49,7 +49,7 @@ def test_badcount():


def test_hashtable_n_entries():
countingtable = khmer.new_hashtable(4, 4 ** 4)
countingtable = khmer.new_hashtable(4, 4)
try:
countingtable.n_entries("nope")
assert 0, "n_entries should accept no arguments"
Expand All @@ -58,7 +58,7 @@ def test_hashtable_n_entries():


def test_complete_no_collision():
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4 ** 2)

for i in range(0, kh.n_entries()):
s = khmer.reverse_hash(i, 4)
Expand All @@ -84,7 +84,7 @@ def test_complete_no_collision():


def test_complete_2_collision():
kh = khmer.new_hashtable(4, 4 ** 4 / 2)
kh = khmer.new_hashtable(4, 4)

for i in range(0, kh.n_entries()):
s = khmer.reverse_hash(i, 4)
Expand All @@ -105,7 +105,7 @@ def test_complete_2_collision():


def test_complete_4_collision():
kh = khmer.new_hashtable(4, 4 ** 4 / 4)
kh = khmer.new_hashtable(4, 2)

for i in range(0, kh.n_entries()):
s = khmer.reverse_hash(i, 4)
Expand All @@ -127,7 +127,7 @@ def test_complete_4_collision():

def test_maxcount():
# hashtable should saturate at some point so as not to overflow counter
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4)

last_count = None
for _ in range(0, 10000):
Expand All @@ -145,7 +145,7 @@ def test_maxcount():

def test_maxcount_with_bigcount():
# hashtable should not saturate, if use_bigcount is set.
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4)
kh.set_use_bigcount(True)

last_count = None
Expand All @@ -163,7 +163,7 @@ def test_maxcount_with_bigcount():


def test_consume_uniqify_first():
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4)

s = "TTTT"
s_rc = "AAAA"
Expand All @@ -175,7 +175,7 @@ def test_consume_uniqify_first():

def test_maxcount_consume():
# hashtable should saturate at some point so as not to overflow counter
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4)

s = "A" * 10000
kh.consume(s)
Expand All @@ -186,7 +186,7 @@ def test_maxcount_consume():

def test_maxcount_consume_with_bigcount():
# use the bigcount hack to avoid saturating the hashtable.
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4)
kh.set_use_bigcount(True)

s = "A" * 10000
Expand All @@ -197,7 +197,7 @@ def test_maxcount_consume_with_bigcount():


def test_get_mincount():
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4)

s = "AAAAACGT"
kh.consume(s)
Expand All @@ -211,7 +211,7 @@ def test_get_mincount():


def test_get_maxcount():
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4)

s = "AAAAACGT"
kh.consume(s)
Expand All @@ -225,7 +225,7 @@ def test_get_maxcount():


def test_get_maxcount_rc():
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4)

s = "AAAAACGT"
src = "ACGTTTTT"
Expand All @@ -240,7 +240,7 @@ def test_get_maxcount_rc():


def test_get_mincount_rc():
kh = khmer.new_hashtable(4, 4 ** 4)
kh = khmer.new_hashtable(4, 4)

s = "AAAAACGT"
src = "ACGTTTTT"
Expand All @@ -255,7 +255,7 @@ def test_get_mincount_rc():


def test_64bitshift():
kh = khmer.new_hashtable(25, 4 ** 10)
kh = khmer.new_hashtable(25, 4)
fullstr = "GTATGCCAGCTCCAACTGGGCCGGTACGAGCAGGCCATTGCCTCTTGCCGCGATGCGTCGGCG"
substr = "ATGCCAGCTCCAACTGGGCCGGTACGAGCAGGCCATTGCCTCTTGC"

Expand All @@ -265,7 +265,7 @@ def test_64bitshift():

@attr('highmem')
def test_64bitshift_2():
kh = khmer.new_hashtable(25, 4 ** 10)
kh = khmer.new_hashtable(25, 4)
fullstr = "GTATGCCAGCTCCAACTGGGCCGGTACGAGCAGGCCATTGCCTCTTGCCGCGATGCGTCGGCG"

kh.consume(fullstr)
Expand All @@ -277,12 +277,12 @@ def test_64bitshift_2():
@attr('highmem')
def test_very_short_read():
short_filename = utils.get_test_data('test-short.fa')
kh = khmer.new_hashtable(9, 4 ** 4 + 1)
kh = khmer.new_hashtable(9, 4)
n_reads, n_kmers = kh.consume_fasta(short_filename)
assert n_reads == 1
assert n_kmers == 0

kh = khmer.new_hashtable(8, 4 ** 4 + 1)
kh = khmer.new_hashtable(8, 4)
n_reads, n_kmers = kh.consume_fasta(short_filename)
assert n_reads == 1
assert n_kmers == 1
Expand Down Expand Up @@ -389,15 +389,15 @@ def test_max_count(self):
class Test_AbundanceDistribution(object):

def setup(self):
self.kh = khmer.new_hashtable(4, 4 ** 4)
self.kh = khmer.new_hashtable(4, 4)
A_filename = utils.get_test_data('all-A.fa')
self.kh.consume_fasta(A_filename)

@attr('highmem')
def test_count_A(self):
A_filename = utils.get_test_data('all-A.fa')

tracking = khmer.new_hashbits(4, 4 ** 4, 1)
tracking = khmer.new_hashbits(4, 4, 1)
dist = self.kh.abundance_distribution(A_filename, tracking)

assert sum(dist) == 1
Expand Down
2 changes: 1 addition & 1 deletion tests/test_subset_graph.py
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Expand Up @@ -195,7 +195,7 @@ class Test_SaveLoadPmap(object):

@attr('highmem')
def test_save_load_merge(self):
ht = khmer.new_hashbits(20, 4 ** 10 + 1)
ht = khmer.new_hashbits(20, 4 ** 4 + 1)
filename = utils.get_test_data('test-graph2.fa')

(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
Expand Down