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# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2010-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project@idyll.org
from __future__ import print_function
from __future__ import absolute_import
import khmer
import screed
from . import khmer_tst_utils as utils
from nose.plugins.attrib import attr
def teardown():
utils.cleanup()
class Test_ExactGraphFu(object):
def setup(self):
self.ht = khmer.Nodegraph(12, 1e4, 2)
def test_counts(self):
ht = self.ht
ht.consume_fasta(utils.get_test_data('test-graph.fa'))
kmer = "TTAGGACTGCAC"
x = ht.calc_connected_graph_size(kmer)
assert x == 69, x
kmer = "TGCGTTTCAATC"
x = ht.calc_connected_graph_size(kmer)
assert x == 68, x
kmer = "ATACTGTAAATA"
x = ht.calc_connected_graph_size(kmer)
assert x == 36, x
def test_graph_links_next_a(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume(word[1:] + "A")
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_next_c(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume(word[1:] + "C")
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_next_g(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume(word[1:] + "G")
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_next_t(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume(word[1:] + "T")
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_prev_a(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume("A" + word[:-1])
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_prev_c(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume("C" + word[:-1])
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_prev_g(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume("G" + word[:-1])
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_prev_t(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume("T" + word[:-1])
x = ht.calc_connected_graph_size(word)
assert x == 2
class Test_InexactGraphFu(object):
def setup(self):
self.ht = khmer.Nodegraph(12, 4 ** 3 + 1, 2)
def test_graph_links_next_a(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume(word[1:] + "A")
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_next_c(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume(word[1:] + "C")
x = ht.calc_connected_graph_size(word)
assert x == 2, x
def test_graph_links_next_g(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume(word[1:] + "G")
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_next_t(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume(word[1:] + "T")
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_prev_a(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume("A" + word[:-1])
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_prev_c(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume("C" + word[:-1])
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_prev_g(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume("G" + word[:-1])
x = ht.calc_connected_graph_size(word)
assert x == 2
def test_graph_links_prev_t(self):
ht = self.ht
word = "TGCGTTTCAATC"
ht.consume(word)
ht.consume("T" + word[:-1])
x = ht.calc_connected_graph_size(word)
assert x == 2
#
class Test_Partitioning(object):
def test_output_unassigned(self):
import screed
filename = utils.get_test_data('random-20-a.fa')
ht = khmer._Nodegraph(21, [5, 7, 11, 13])
ht.consume_fasta_and_tag(filename)
output_file = utils.get_temp_filename('part0test')
ht.output_partitions(filename, output_file, True)
len1 = len(list(screed.open(filename)))
len2 = len(list(screed.open(output_file)))
assert len1 > 0
assert len1 == len2, (len1, len2)
def test_not_output_unassigned(self):
import screed
filename = utils.get_test_data('random-20-a.fa')
ht = khmer._Nodegraph(21, [5, 7, 11, 13])
ht.consume_fasta_and_tag(filename)
output_file = utils.get_temp_filename('parttest')
ht.output_partitions(filename, output_file, False)
len1 = len(list(screed.open(filename)))
len2 = len(list(screed.open(output_file)))
assert len1 > 0
assert len2 == 0, len2
def test_output_fq(self):
filename = utils.get_test_data('random-20-a.fq')
ht = khmer.Nodegraph(20, 1e4, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
output_file = utils.get_temp_filename('parttest')
ht.output_partitions(filename, output_file, False)
print(open(output_file).read())
x = set([r.quality for r in screed.open(output_file)])
assert x, x
def test_disconnected_20_a(self):
filename = utils.get_test_data('random-20-a.fa')
ht = khmer.Nodegraph(21, 1e5, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
assert x == (99, 0), x # disconnected @ 21
def test_connected_20_a(self):
filename = utils.get_test_data('random-20-a.fa')
ht = khmer.Nodegraph(20, 1e4, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
assert x == (1, 0) # connected @ 20
def test_disconnected_20_b(self):
filename = utils.get_test_data('random-20-b.fa')
ht = khmer.Nodegraph(21, 1e4, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
assert x == (99, 0), x # disconnected @ 21
def test_connected_20_b(self):
filename = utils.get_test_data('random-20-b.fa')
ht = khmer.Nodegraph(20, 1e4, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
assert x == (1, 0) # connected @ 20
def test_disconnected_31_c(self):
filename = utils.get_test_data('random-31-c.fa')
ht = khmer.Nodegraph(32, 1e6, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
assert x == (999, 0), x # disconnected @ K = 32
def test_connected_31_c(self):
filename = utils.get_test_data('random-31-c.fa')
ht = khmer.Nodegraph(31, 1e5, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
assert x == (1, 0) # connected @ K = 31
#
class Test_PythonAPI(object):
def test_find_all_tags_kmersize(self):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
a = "ATTGGGACTCTGGGAGCACTTATCATGGAGAT"
b = "GAGCACTTTAACCCTGCAGAGTGGCCAAGGCT"
c = "GGAGCACTTATCATGGAGATATATCCCGTGCTTAAACATCGCACTTTAACCCTGCAGAGT"
print(ht.consume(a))
try:
ppi = ht.find_all_tags(c[:19])
assert False, "should raise a ValueError for wrong k-mer size"
except ValueError:
pass
try:
ppi = ht.find_all_tags(c[:21])
assert False, "should raise a ValueError for wrong k-mer size"
except ValueError:
pass
def test_ordered_connect(self):
ht = khmer.Nodegraph(20, 4 ** 4 + 1, 2)
a = "ATTGGGACTCTGGGAGCACTTATCATGGAGAT"
b = "GAGCACTTTAACCCTGCAGAGTGGCCAAGGCT"
c = "GGAGCACTTATCATGGAGATATATCCCGTGCTTAAACATCGCACTTTAACCCTGCAGAGT"
print(ht.consume(a))
ppi = ht.find_all_tags(a[:20])
pid = ht.assign_partition_id(ppi)
assert pid == 0, pid
print(ht.consume(b))
ppi = ht.find_all_tags(b[:20])
pid = ht.assign_partition_id(ppi)
assert pid == 0, pid
print(ht.consume(c))
ppi = ht.find_all_tags(c[:20])
pid = ht.assign_partition_id(ppi)
assert pid == 2, pid
#
|
