def test_normalize_by_median_dumpfrequency():
CUTOFF = '1'
infiles = [utils.get_temp_filename('test-0.fq')]
in_dir = os.path.dirname(infiles[0])
for x in range(1, 5):
infiles.append(
utils.get_temp_filename('test-{x}.fq'.format(x=x), tempdir=in_dir))
for infile in infiles:
shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), infile)
script = scriptpath('normalize-by-median.py')
args = ['-d', '2', '-C', CUTOFF, '-k', '17']
args.extend(infiles)
(status, out, err) = utils.runscript(script, args, in_dir)
test_ht = khmer.load_counting_hash(os.path.join(in_dir, 'backup.ct'))
test_good_read = 'CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT'
test_good_read2 = 'TAGTATCATCAAGGTTCAAGATGTTAATGAATAACAATTGCGCAGCAA'
assert test_ht.count(test_good_read[:17]) > 0
assert test_ht.count(test_good_read2[:17]) > 0
assert os.path.exists(os.path.join(in_dir, 'backup.ct'))
assert out.count('Backup: Saving') == 2
assert 'Nothing' in out
def test_split_paired_reads_1_fa():
# test input file
infile = utils.get_test_data("paired.fa")
ex_outfile1 = utils.get_test_data("paired.fa.1")
ex_outfile2 = utils.get_test_data("paired.fa.2")
# actual output files...
outfile1 = utils.get_temp_filename("paired.fa.1")
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename("paired.fa.2", in_dir)
script = scriptpath("split-paired-reads.py")
args = [infile]
runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_filter_stoptags():
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
stopfile = utils.get_temp_filename('stoptags', in_dir)
# first, copy test-abund-read-2.fa to 'test.fa' in the temp dir.
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
# now, create a file with some stop tags in it --
K = 18
kh = khmer.new_hashbits(K, 1, 1)
kh.add_stop_tag('GTTGACGGGGCTCAGGGG')
kh.save_stop_tags(stopfile)
del kh
# finally, run filter-stoptags.
script = scriptpath('filter-stoptags.py')
args = ['-k', str(K), stopfile, infile, infile]
utils.runscript(script, args, in_dir)
# verify that the basic output file exists
outfile = infile + '.stopfilt'
assert os.path.exists(outfile), outfile
# it should contain only one unique sequence, because we've trimmed
# off everything after the beginning of the only long sequence in there.
seqs = set([r.sequence for r in screed.open(outfile)])
assert len(seqs) == 1, seqs
assert 'GGTTGACGGGGCTCAGGG' in seqs, seqs
def test_normalize_by_median_force():
CUTOFF = '1'
corrupt_infile = utils.get_temp_filename('test-corrupt.fq')
good_infile = utils.get_temp_filename(
'test-good.fq', tempdir=os.path.dirname(corrupt_infile))
in_dir = os.path.dirname(good_infile)
shutil.copyfile(utils.get_test_data('test-error-reads.fq'), corrupt_infile)
shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), good_infile)
script = scriptpath('normalize-by-median.py')
args = ['-f', '-C', CUTOFF, '-k', '17', corrupt_infile, good_infile]
(status, out, err) = utils.runscript(script, args, in_dir)
test_ht = khmer.load_counting_hash(corrupt_infile + '.ct.failed')
test_good_read = 'CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT'
test_good_read2 = 'TAGTATCATCAAGGTTCAAGATGTTAATGAATAACAATTGCGCAGCAA'
assert test_ht.count(test_good_read[:17]) > 0
assert test_ht.count(test_good_read2[:17]) > 0
assert os.path.exists(corrupt_infile + '.ct.failed')
assert '*** Skipping' in err
assert '** IOErrors' in err
def test_extract_long_sequences():
script = scriptpath('extract-long-sequences.py')
fq_infile = utils.get_temp_filename('test.fq')
fa_infile = utils.get_temp_filename('test.fa')
shutil.copyfile(utils.get_test_data('paired-mixed.fq'), fq_infile)
shutil.copyfile(utils.get_test_data('paired-mixed.fa'), fa_infile)
fq_outfile = fq_infile + '.keep.fq'
fa_outfile = fa_infile + '.keep.fa'
in_dir_fq = os.path.dirname(fq_infile)
in_dir_fa = os.path.dirname(fa_infile)
args = [fq_infile, '-l', '10', '-o', 'fq_outfile']
(status, out, err) = utils.runscript(script, args, in_dir_fa)
countlines = sum(1 for line in open(fq_infile))
assert countlines == 44, countlines
args = [fa_infile, '-l', '10', '-o', 'fa_outfile']
(status, out, err) = utils.runscript(script, args, in_dir_fa)
countlines = sum(1 for line in open(fa_infile))
assert countlines == 22, countlines
def test_count_overlap():
seqfile1 = utils.get_temp_filename('test-overlap1.fa')
in_dir = os.path.dirname(seqfile1)
seqfile2 = utils.get_temp_filename('test-overlap2.fa', in_dir)
outfile = utils.get_temp_filename('overlap.out', in_dir)
curvefile = utils.get_temp_filename('overlap.out.curve', in_dir)
shutil.copy(utils.get_test_data('test-overlap1.fa'), seqfile1)
shutil.copy(utils.get_test_data('test-overlap2.fa'), seqfile2)
htfile = _make_graph(seqfile1, ksize=20)
script = scriptpath('count-overlap.py')
args = [
'--ksize', '20', '--n_tables', '2', '--min-tablesize', '10000000',
htfile + '.pt', seqfile2, outfile
]
(status, out, err) = utils.runscript(script, args, in_dir)
assert status == 0
assert os.path.exists(outfile), outfile
data = [x.strip() for x in open(outfile)]
data = set(data)
assert '# of unique k-mers in dataset2: 759047' in data
assert '# of overlap unique k-mers: 245621' in data
assert os.path.exists(curvefile), curvefile
data = [x.strip() for x in open(curvefile)]
data = set(data)
assert '178633 1155' in data
assert '496285 2970' in data
assert '752053 238627' in data
def test_split_paired_reads_2_fq():
# test input file
infile = utils.get_test_data('paired.fq')
ex_outfile1 = utils.get_test_data('paired.fq.1')
ex_outfile2 = utils.get_test_data('paired.fq.2')
# actual output files...
outfile1 = utils.get_temp_filename('paired.fq.1')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired.fq.2', in_dir)
script = scriptpath('split-paired-reads.py')
args = [infile]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.accuracy == q.accuracy
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.accuracy == q.accuracy
assert n > 0
def test_extract_paired_reads_1_fa():
# test input file
infile = utils.get_test_data('paired-mixed.fa')
ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
# actual output files...
outfile1 = utils.get_temp_filename('paired-mixed.fa.pe')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired-mixed.fa.se', in_dir)
script = scriptpath('extract-paired-reads.py')
args = [infile]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_make_initial_stoptags():
# gen input files using load-graph.py -t
# should keep test_data directory size down
# or something like that
# this assumes (obv.) load-graph works properly
bzinfile = utils.get_temp_filename('test-reads.fq.bz2')
shutil.copyfile(utils.get_test_data('test-reads.fq.bz2'), bzinfile)
in_dir = os.path.dirname(bzinfile)
genscript = scriptpath('load-graph.py')
genscriptargs = ['-t', 'test-reads', 'test-reads.fq.bz2']
utils.runscript(genscript, genscriptargs, in_dir)
# test input file gen'd by load-graphs
infile = utils.get_temp_filename('test-reads.pt')
infile2 = utils.get_temp_filename('test-reads.tagset', in_dir)
# get file to compare against
ex_outfile = utils.get_test_data('test-reads.stoptags')
# actual output file
outfile1 = utils.get_temp_filename('test-reads.stoptags', in_dir)
script = scriptpath('make-initial-stoptags.py')
# make-initial-stoptags has weird file argument syntax
# read the code before modifying
args = ['test-reads']
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
def test_normalize_by_median_dumpfrequency():
CUTOFF = "1"
infiles = [utils.get_temp_filename("test-0.fq")]
in_dir = os.path.dirname(infiles[0])
for x in range(1, 5):
infiles.append(utils.get_temp_filename("test-{x}.fq".format(x=x), tempdir=in_dir))
for infile in infiles:
shutil.copyfile(utils.get_test_data("test-fastq-reads.fq"), infile)
script = scriptpath("normalize-by-median.py")
args = ["-d", "2", "-C", CUTOFF, "-k", "17"]
args.extend(infiles)
(status, out, err) = runscript(script, args, in_dir)
test_ht = khmer.load_counting_hash(os.path.join(in_dir, "backup.ht"))
test_good_read = "CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT"
test_good_read2 = "TAGTATCATCAAGGTTCAAGATGTTAATGAATAACAATTGCGCAGCAA"
assert test_ht.count(test_good_read[:17]) > 0
assert test_ht.count(test_good_read2[:17]) > 0
assert os.path.exists(os.path.join(in_dir, "backup.ht"))
assert out.count("Backup: Saving") == 2
assert "Nothing" in out
def test_save_merge_from_disk(self):
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)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print divvy
(a, b, c) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
x = ht.do_subset_partition(a, b)
ht.save_subset_partitionmap(x, outfile1)
del x
y = ht.do_subset_partition(b, 0)
ht.save_subset_partitionmap(y, outfile2)
del y
ht.merge_subset_from_disk(outfile1)
ht.merge_subset_from_disk(outfile2)
outfile = utils.get_temp_filename('out.part')
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
def test_save_load_merge(self):
raise Exception("this test coredumps on lyorn. Disabled.")
ht = khmer.new_hashbits(20, 4**14+1)
filename = utils.get_test_data('test-graph2.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print divvy
(a, b, c) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
x = ht.do_subset_partition(a, b)
ht.save_subset_partitionmap(x, outfile1)
del x
y = ht.do_subset_partition(b, 0)
ht.save_subset_partitionmap(y, outfile2)
del y
a = ht.load_subset_partitionmap(outfile1)
b = ht.load_subset_partitionmap(outfile2)
ht.merge_subset(a)
ht.merge_subset(b)
outfile = utils.get_temp_filename('out.part')
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
def test_abund_dist_gz_bigcount():
infile = utils.get_temp_filename('test.fa')
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
outfile = utils.get_temp_filename('test_ct.gz')
script = scriptpath('load-into-counting.py')
htfile = utils.get_temp_filename('test_ct')
args = ['-x', str(1e7), '-N', str(2), '-k', str(2), htfile, infile]
utils.runscript(script, args) # create a bigcount table
assert os.path.exists(htfile)
data = open(htfile, 'rb').read()
f_out = gzip.open(outfile, 'wb') # compress the created bigcount table
f_out.write(data)
f_out.close()
# load the compressed bigcount table
counting_hash = khmer.load_counting_hash(outfile)
hashsizes = counting_hash.hashsizes()
kmer_size = counting_hash.ksize()
tracking = khmer._Hashbits(kmer_size, hashsizes)
abundances = counting_hash.abundance_distribution(infile, tracking)
# calculate abundance distribution for compressed bigcount table
flag = False
# check if abundance is > 255
# if ok gzipped bigcount was loaded correctly
for _, i in enumerate(abundances):
print _, i
if _ > 255 and i > 0:
flag = True
break
assert flag
def test_save_merge_from_disk_2(self):
raise Exception("this test coredumps on lyorn. Disabled.")
ht = khmer.new_hashbits(20, 4**14 + 1)
filename = utils.get_test_data('random-20-a.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
subset_size = total_reads / 2 + total_reads % 2
divvy = ht.divide_tags_into_subsets(subset_size)
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
x = ht.do_subset_partition(divvy[0], divvy[1])
ht.save_subset_partitionmap(x, outfile1)
del x
y = ht.do_subset_partition(divvy[1], 0)
ht.save_subset_partitionmap(y, outfile2)
del y
ht.merge_subset_from_disk(outfile1)
ht.merge_subset_from_disk(outfile2)
outfile = utils.get_temp_filename('out.part')
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
def test_save_load_corrupted():
lb_pre = LabelHash(20, 1e7, 4)
filename = utils.get_test_data('test-labels.fa')
lb_pre.consume_fasta_and_tag_with_labels(filename)
# save labels to a file
savepath = utils.get_temp_filename('saved.labels')
lb_pre.save_labels_and_tags(savepath)
# trash the old LabelHash
del lb_pre
lb = LabelHash(20, 1e7, 4)
# produce all possible truncated versions of this file
data = open(savepath, 'rb').read()
for i in range(len(data)):
truncated = utils.get_temp_filename('trunc.labels')
fp = open(truncated, 'wb')
fp.write(data[:i])
fp.close()
try:
lb.load_labels_and_tags(truncated)
assert 0, "this should not succeed -- truncated file len %d" % (i,)
except IOError as err:
print 'expected failure for', i, ': ', str(err)
def test_save_merge_from_disk(self):
raise Exception("this test coredumps on lyorn. Disabled.")
ht = khmer.new_hashbits(20, 4**14 + 1)
filename = utils.get_test_data('test-graph2.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print divvy
(a, b, c) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
x = ht.do_subset_partition(a, b)
ht.save_subset_partitionmap(x, outfile1)
del x
y = ht.do_subset_partition(b, 0)
ht.save_subset_partitionmap(y, outfile2)
del y
ht.merge_subset_from_disk(outfile1)
ht.merge_subset_from_disk(outfile2)
outfile = utils.get_temp_filename('out.part')
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
def test_random_20_a_succ_IV_save(self):
ht = khmer.new_hashbits(20, 4**13 + 1)
filename = utils.get_test_data('random-20-a.fa')
savefile_ht = utils.get_temp_filename('ht')
savefile_tags = utils.get_temp_filename('tags')
outfile = filename + utils.get_temp_filename('out')
total_reads, _ = ht.consume_fasta_and_tag(filename)
ht.save(savefile_ht)
ht.save_tagset(savefile_tags)
del ht
ht = khmer.new_hashbits(20, 4**13 + 1)
ht.load(savefile_ht)
ht.load_tagset(savefile_tags)
divvy = ht.divide_tags_into_subsets(1)
divvy.append(0)
subsets = []
for i in range(len(divvy) - 1):
x = ht.do_subset_partition(divvy[i], divvy[i + 1])
subsets.append(x)
for x in reversed(subsets):
ht.merge_subset(x)
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions
def test_save_load_merge_2(self):
ht = khmer.new_hashbits(20, 4**8 + 1)
filename = utils.get_test_data('random-20-a.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
subset_size = total_reads // 2 + total_reads % 2
divvy = ht.divide_tags_into_subsets(subset_size)
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
x = ht.do_subset_partition(divvy[0], divvy[1])
ht.save_subset_partitionmap(x, outfile1)
del x
y = ht.do_subset_partition(divvy[1], 0)
ht.save_subset_partitionmap(y, outfile2)
del y
assert os.path.exists(outfile1)
assert os.path.exists(outfile2)
a = ht.load_subset_partitionmap(outfile1)
b = ht.load_subset_partitionmap(outfile2)
ht.merge_subset(a)
ht.merge_subset(b)
outfile = utils.get_temp_filename('out.part')
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
def test_load_gz():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave1.ht')
loadpath = utils.get_temp_filename('tempcountingsave1.ht.gz')
sizes = list(PRIMES_1m)
sizes.append(1000005)
# save uncompressed hashtable.
hi = khmer._new_counting_hash(12, sizes)
hi.consume_fasta(inpath)
hi.save(savepath)
# compress.
in_file = open(savepath, 'rb')
out_file = gzip.open(loadpath, 'wb')
out_file.writelines(in_file)
out_file.close()
in_file.close()
# load compressed hashtable.
ht = khmer._new_counting_hash(12, sizes)
ht.load(loadpath)
tracking = khmer._new_hashbits(12, sizes)
x = hi.abundance_distribution(inpath, tracking)
tracking = khmer._new_hashbits(12, sizes)
y = ht.abundance_distribution(inpath, tracking)
assert sum(x) == 3966, sum(x)
assert x == y, (x, y)
def test_abund_dist_gz_bigcount():
infile = utils.get_temp_filename('test.fa')
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
outfile = utils.get_temp_filename('test_ct.gz')
script = scriptpath('load-into-counting.py')
htfile = utils.get_temp_filename('test_ct')
args = ['-x', str(1e7), '-N', str(2), '-k', str(2), htfile, infile]
utils.runscript(script, args) # create a bigcount table
assert os.path.exists(htfile)
data = open(htfile, 'rb').read()
f_out = gzip.open(outfile, 'wb') # compress the created bigcount table
f_out.write(data)
f_out.close()
# load the compressed bigcount table
counting_hash = khmer.load_counting_hash(outfile)
hashsizes = counting_hash.hashsizes()
kmer_size = counting_hash.ksize()
tracking = khmer._Hashbits(kmer_size, hashsizes)
abundances = counting_hash.abundance_distribution(infile, tracking)
# calculate abundance distribution for compressed bigcount table
flag = False
# check if abundance is > 255
# if ok gzipped bigcount was loaded correctly
for _, i in enumerate(abundances):
print _, i
if _ > 255 and i > 0:
flag = True
break
assert flag
def test_save_load_merge_on_graph():
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)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print divvy
assert len(divvy) is 3
(a, b, c) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
x = ht.do_subset_partition(a, b)
ht.save_subset_partitionmap(x, outfile1)
del x
y = ht.do_subset_partition(b, 0)
ht.save_subset_partitionmap(y, outfile2)
del y
a = ht.load_partitionmap(outfile1) # <-- this is different
b = ht.load_subset_partitionmap(outfile2)
ht.merge_subset(b)
outfile = utils.get_temp_filename('out.part')
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
def test_normalize_by_median_dumpfrequency():
CUTOFF = '1'
infiles = [utils.get_temp_filename('test-0.fq')]
in_dir = os.path.dirname(infiles[0])
for x in range(1, 5):
infiles.append(utils.get_temp_filename('test-{x}.fq'.format(x=x),
tempdir=in_dir))
for infile in infiles:
shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), infile)
script = scriptpath('normalize-by-median.py')
args = ['-d', '2', '-C', CUTOFF, '-k', '17']
args.extend(infiles)
(status, out, err) = runscript(script, args, in_dir)
test_ht = khmer.load_counting_hash(os.path.join(in_dir, 'backup.ct'))
test_good_read = 'CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT'
test_good_read2 = 'TAGTATCATCAAGGTTCAAGATGTTAATGAATAACAATTGCGCAGCAA'
assert test_ht.count(test_good_read[:17]) > 0
assert test_ht.count(test_good_read2[:17]) > 0
assert os.path.exists(os.path.join(in_dir, 'backup.ct'))
assert out.count('Backup: Saving') == 2
assert 'Nothing' in out
def test_extract_paired_reads_1_fa():
# test input file
infile = utils.get_test_data('paired-mixed.fa')
ex_outfile1 = utils.get_test_data('paired-mixed.fa.pe')
ex_outfile2 = utils.get_test_data('paired-mixed.fa.se')
# actual output files...
outfile1 = utils.get_temp_filename('paired-mixed.fa.pe')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired-mixed.fa.se', in_dir)
script = scriptpath('extract-paired-reads.py')
args = [infile]
runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert n > 0
def test_make_initial_stoptags():
# gen input files using load-graph.py -t
# should keep test_data directory size down
# or something like that
# this assumes (obv.) load-graph works properly
bzinfile = utils.get_temp_filename('test-reads.fq.bz2')
shutil.copyfile(utils.get_test_data('test-reads.fq.bz2'), bzinfile)
in_dir = os.path.dirname(bzinfile)
genscript = scriptpath('load-graph.py')
genscriptargs = ['-t', 'test-reads', 'test-reads.fq.bz2']
utils.runscript(genscript, genscriptargs, in_dir)
# test input file gen'd by load-graphs
infile = utils.get_temp_filename('test-reads.pt')
infile2 = utils.get_temp_filename('test-reads.tagset', in_dir)
# get file to compare against
ex_outfile = utils.get_test_data('test-reads.stoptags')
# actual output file
outfile1 = utils.get_temp_filename('test-reads.stoptags', in_dir)
script = scriptpath('make-initial-stoptags.py')
# make-initial-stoptags has weird file argument syntax
# read the code before modifying
args = ['test-reads']
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
def test_random_20_a_succ_IV_save(self):
ht = khmer.new_hashbits(20, 4 ** 7 + 1)
filename = utils.get_test_data('random-20-a.fa')
savefile_ht = utils.get_temp_filename('ht')
savefile_tags = utils.get_temp_filename('tags')
outfile = filename + utils.get_temp_filename('out')
total_reads, _ = ht.consume_fasta_and_tag(filename)
ht.save(savefile_ht)
ht.save_tagset(savefile_tags)
del ht
ht = khmer.new_hashbits(20, 4 ** 7 + 1)
ht.load(savefile_ht)
ht.load_tagset(savefile_tags)
divvy = ht.divide_tags_into_subsets(1)
divvy.append(0)
subsets = []
for i in range(len(divvy) - 1):
x = ht.do_subset_partition(divvy[i], divvy[i + 1])
subsets.append(x)
for x in reversed(subsets):
ht.merge_subset(x)
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions
def test_save_load_merge(self):
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)
assert total_reads == 3, total_reads
divvy = ht.divide_tags_into_subsets(1)
print divvy
assert len(divvy) is 3
(a, b, c) = divvy
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
x = ht.do_subset_partition(a, b)
ht.save_subset_partitionmap(x, outfile1)
del x
y = ht.do_subset_partition(b, 0)
ht.save_subset_partitionmap(y, outfile2)
del y
a = ht.load_subset_partitionmap(outfile1)
b = ht.load_subset_partitionmap(outfile2)
ht.merge_subset(a)
ht.merge_subset(b)
outfile = utils.get_temp_filename('out.part')
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
def test_filter_stoptags():
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
stopfile = utils.get_temp_filename('stoptags', in_dir)
# first, copy test-abund-read-2.fa to 'test.fa' in the temp dir.
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
# now, create a file with some stop tags in it --
K = 18
kh = khmer.new_hashbits(K, 1, 1)
kh.add_stop_tag('GTTGACGGGGCTCAGGGG')
kh.save_stop_tags(stopfile)
del kh
# finally, run filter-stoptags.
script = scriptpath('filter-stoptags.py')
args = ['-k', str(K), stopfile, infile, infile]
(status, out, err) = runscript(script, args, in_dir)
print out
print err
assert status == 0
# verify that the basic output file exists
outfile = infile + '.stopfilt'
assert os.path.exists(outfile), outfile
# it should contain only one unique sequence, because we've trimmed
# off everything after the beginning of the only long sequence in there.
seqs = set([ r.sequence for r in screed.open(outfile) ])
assert len(seqs) == 1, seqs
assert 'GGTTGACGGGGCTCAGGG' in seqs, seqs
def test_save_load_merge_2(self):
raise Exception("this test coredumps on lyorn. Disabled.")
ht = khmer.new_hashbits(20, 4**14+1)
filename = utils.get_test_data('random-20-a.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
subset_size = total_reads / 2 + total_reads % 2;
divvy = ht.divide_tags_into_subsets(subset_size)
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
x = ht.do_subset_partition(divvy[0], divvy[1])
ht.save_subset_partitionmap(x, outfile1)
del x
y = ht.do_subset_partition(divvy[1], 0)
ht.save_subset_partitionmap(y, outfile2)
del y
a = ht.load_subset_partitionmap(outfile1)
b = ht.load_subset_partitionmap(outfile2)
ht.merge_subset(a)
ht.merge_subset(b)
outfile = utils.get_temp_filename('out.part')
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
def test_count_overlap():
seqfile1 = utils.get_temp_filename('test-overlap1.fa')
in_dir = os.path.dirname(seqfile1)
seqfile2 = utils.get_temp_filename('test-overlap2.fa', in_dir)
outfile = utils.get_temp_filename('overlap.out', in_dir)
curvefile = utils.get_temp_filename('overlap.out.curve', in_dir)
shutil.copy(utils.get_test_data('test-overlap1.fa'), seqfile1)
shutil.copy(utils.get_test_data('test-overlap2.fa'), seqfile2)
htfile = _make_graph(seqfile1, ksize=20)
script = scriptpath('count-overlap.py')
args = ['--ksize', '20', '--n_tables', '2', '--min-tablesize', '10000000',
htfile + '.pt', seqfile2, outfile]
(status, out, err) = runscript(script, args, in_dir)
assert status == 0
assert os.path.exists(outfile), outfile
data = [x.strip() for x in open(outfile)]
data = set(data)
assert '# of unique k-mers in dataset2: 759047' in data
assert '# of overlap unique k-mers: 245621' in data
assert os.path.exists(curvefile), curvefile
data = [x.strip() for x in open(curvefile)]
data = set(data)
assert '178633 1155' in data
assert '496285 2970' in data
assert '752053 238627' in data
def test_split_paired_reads_2_fq():
# test input file
infile = utils.get_test_data('paired.fq')
ex_outfile1 = utils.get_test_data('paired.fq.1')
ex_outfile2 = utils.get_test_data('paired.fq.2')
# actual output files...
outfile1 = utils.get_temp_filename('paired.fq.1')
in_dir = os.path.dirname(outfile1)
outfile2 = utils.get_temp_filename('paired.fq.2', in_dir)
script = scriptpath('split-paired-reads.py')
args = [infile]
runscript(script, args, in_dir)
assert os.path.exists(outfile1), outfile1
assert os.path.exists(outfile2), outfile2
n = 0
for r, q in zip(screed.open(ex_outfile1), screed.open(outfile1)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.accuracy == q.accuracy
assert n > 0
n = 0
for r, q in zip(screed.open(ex_outfile2), screed.open(outfile2)):
n += 1
assert r.name == q.name
assert r.sequence == q.sequence
assert r.accuracy == q.accuracy
assert n > 0
def test_save_merge_from_disk_2(self):
ht = khmer.new_hashbits(20, 4 ** 7 + 1)
filename = utils.get_test_data('random-20-a.fa')
(total_reads, total_kmers) = ht.consume_fasta_and_tag(filename)
subset_size = total_reads // 2 + total_reads % 2
divvy = ht.divide_tags_into_subsets(subset_size)
outfile1 = utils.get_temp_filename('x.pmap')
outfile2 = utils.get_temp_filename('y.pmap')
x = ht.do_subset_partition(divvy[0], divvy[1])
ht.save_subset_partitionmap(x, outfile1)
del x
y = ht.do_subset_partition(divvy[1], 0)
ht.save_subset_partitionmap(y, outfile2)
del y
ht.merge_subset_from_disk(outfile1)
ht.merge_subset_from_disk(outfile2)
outfile = utils.get_temp_filename('out.part')
n_partitions = ht.output_partitions(filename, outfile)
assert n_partitions == 1, n_partitions # combined.
def test_extract_long_sequences():
script = scriptpath('extract-long-sequences.py')
fq_infile = utils.get_temp_filename('test.fq')
fa_infile = utils.get_temp_filename('test.fa')
shutil.copyfile(utils.get_test_data('paired-mixed.fq'), fq_infile)
shutil.copyfile(utils.get_test_data('paired-mixed.fa'), fa_infile)
fq_outfile = fq_infile + '.keep.fq'
fa_outfile = fa_infile + '.keep.fa'
in_dir_fq = os.path.dirname(fq_infile)
in_dir_fa = os.path.dirname(fa_infile)
args = [fq_infile, '-l', '10', '-o', 'fq_outfile']
(status, out, err) = runscript(script, args, in_dir_fa)
countlines = sum(1 for line in open(fq_infile))
assert countlines == 44, countlines
args = [fa_infile, '-l', '10', '-o', 'fa_outfile']
(status, out, err) = runscript(script, args, in_dir_fa)
countlines = sum(1 for line in open(fa_infile))
assert countlines == 22, countlines
def test_load_gz():
inpath = utils.get_test_data('random-20-a.fa')
savepath = utils.get_temp_filename('tempcountingsave1.ht')
loadpath = utils.get_temp_filename('tempcountingsave1.ht.gz')
sizes = list(PRIMES_1m)
sizes.append(1000005)
# save uncompressed hashtable.
hi = khmer._new_counting_hash(12, sizes)
hi.consume_fasta(inpath)
hi.save(savepath)
# compress.
in_file = open(savepath, 'rb')
out_file = gzip.open(loadpath, 'wb')
out_file.writelines(in_file)
out_file.close()
in_file.close()
# load compressed hashtable.
ht = khmer._new_counting_hash(12, sizes)
ht.load(loadpath)
tracking = khmer._new_hashbits(12, sizes)
x = hi.abundance_distribution(inpath, tracking)
tracking = khmer._new_hashbits(12, sizes)
y = ht.abundance_distribution(inpath, tracking)
assert sum(x) == 3966, sum(x)
assert x == y, (x, y)
def test_normalize_by_median_force():
CUTOFF = '1'
corrupt_infile = utils.get_temp_filename('test-corrupt.fq')
good_infile = utils.get_temp_filename('test-good.fq',
tempdir=os.path.dirname(
corrupt_infile))
in_dir = os.path.dirname(good_infile)
shutil.copyfile(utils.get_test_data('test-error-reads.fq'), corrupt_infile)
shutil.copyfile(utils.get_test_data('test-fastq-reads.fq'), good_infile)
script = scriptpath('normalize-by-median.py')
args = ['-f', '-C', CUTOFF, '-k', '17', corrupt_infile, good_infile]
(status, out, err) = runscript(script, args, in_dir)
test_ht = khmer.load_counting_hash(corrupt_infile + '.ct.failed')
test_good_read = 'CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT'
test_good_read2 = 'TAGTATCATCAAGGTTCAAGATGTTAATGAATAACAATTGCGCAGCAA'
assert test_ht.count(test_good_read[:17]) > 0
assert test_ht.count(test_good_read2[:17]) > 0
assert os.path.exists(corrupt_infile + '.ct.failed')
assert '*** Skipping' in err
assert '** IOErrors' in err
def test_sweep_reads_fq():
readfile = utils.get_temp_filename('reads.fa')
contigfile = utils.get_temp_filename('contigs.fp')
in_dir = os.path.dirname(contigfile)
shutil.copyfile(utils.get_test_data('test-sweep-reads.fq'), readfile)
shutil.copyfile(utils.get_test_data('test-sweep-contigs.fp'), contigfile)
script = scriptpath('sweep-reads.py')
args = [
'-k', '25', '--prefix', 'test', '--label-by-pid', contigfile, readfile,
'junkfile.fa'
]
status, out, err = utils.runscript(script,
args,
in_dir,
fail_ok=True,
sandbox=True)
# check if the bad file was skipped without issue
assert 'ERROR' in err, err
assert 'skipping' in err, err
out1 = os.path.join(in_dir, 'test_0.fq')
out2 = os.path.join(in_dir, 'test_1.fq')
mout = os.path.join(in_dir, 'test_multi.fq')
oout = os.path.join(in_dir, 'test_orphaned.fq')
assert os.path.exists(out1)
assert os.path.exists(out2)
assert os.path.exists(mout)
assert os.path.exists(oout)
print open(out1).read()
print os.listdir(in_dir)
seqs1 = set([r.name for r in screed.open(out1)])
seqs2 = set([r.name for r in screed.open(out2)])
seqsm = set([r.name for r in screed.open(mout)])
seqso = set([r.name for r in screed.open(oout)])
print seqs1
print seqs2
print seqsm
print seqso
assert seqs1 == set(['read1_p0\t0', 'read2_p0\t0'])
assert seqs2 == set(['read3_p1\t1'])
assert (seqsm == set(['read4_multi\t0\t1'])
or seqsm == set(['read4_multi\t1\t0']))
assert seqso == set(['read5_orphan'])
seqs1 = set([r.quality for r in screed.open(out1)])
seqs2 = set([r.quality for r in screed.open(out2)])
seqsm = set([r.quality for r in screed.open(mout)])
seqso = set([r.quality for r in screed.open(oout)])
def test_sweep_reads_fq():
readfile = utils.get_temp_filename('reads.fa')
contigfile = utils.get_temp_filename('contigs.fp')
in_dir = os.path.dirname(contigfile)
shutil.copyfile(utils.get_test_data('test-sweep-reads.fq'), readfile)
shutil.copyfile(utils.get_test_data('test-sweep-contigs.fp'), contigfile)
script = scriptpath('sweep-reads.py')
args = ['-k', '25', '--prefix', 'test', '--label-by-pid',
contigfile, readfile, 'junkfile.fa']
status, out, err = utils.runscript(
script, args, in_dir, fail_ok=True, sandbox=True)
# check if the bad file was skipped without issue
assert 'ERROR' in err, err
assert 'skipping' in err, err
out1 = os.path.join(in_dir, 'test_0.fq')
out2 = os.path.join(in_dir, 'test_1.fq')
mout = os.path.join(in_dir, 'test_multi.fq')
oout = os.path.join(in_dir, 'test_orphaned.fq')
assert os.path.exists(out1)
assert os.path.exists(out2)
assert os.path.exists(mout)
assert os.path.exists(oout)
print open(out1).read()
print os.listdir(in_dir)
seqs1 = set([r.name for r in screed.open(out1)])
seqs2 = set([r.name for r in screed.open(out2)])
seqsm = set([r.name for r in screed.open(mout)])
seqso = set([r.name for r in screed.open(oout)])
print seqs1
print seqs2
print seqsm
print seqso
assert seqs1 == set(['read1_p0\t0', 'read2_p0\t0'])
assert seqs2 == set(['read3_p1\t1'])
assert (seqsm == set(['read4_multi\t0\t1']) or
seqsm == set(['read4_multi\t1\t0']))
assert seqso == set(['read5_orphan'])
seqs1 = set([r.quality for r in screed.open(out1)])
seqs2 = set([r.quality for r in screed.open(out2)])
seqsm = set([r.quality for r in screed.open(mout)])
seqso = set([r.quality for r in screed.open(oout)])
def test_save_no_load(self):
filename = utils.get_temp_filename('tst')
rt = self.rt
rt.set(0, True)
rt.set(1, False)
rt.set(2, True)
rt.set(3, False)
rt.set(4, True)
rt.save(filename)
rt2 = khmer.new_readmask(READTABLE_SIZE)
# no load!
try:
for i in range(5):
if rt.get(i) != rt2.get(i):
raise Exception # supposed to happen; no load.
assert 0
except AssertionError:
raise
except Exception:
pass
def test_save_no_load(self):
filename = utils.get_temp_filename('save')
mmt = self.mmt
for i in range(0, MINMAXTABLE_SIZE):
mmt.add_min(i, i)
mmt.add_max(i, MINMAXTABLE_SIZE - i)
mmt.save(filename)
mmt2 = khmer.new_minmax(MINMAXTABLE_SIZE)
# no load!
try:
for i in range(0, MINMAXTABLE_SIZE):
if mmt2.get_min(i) != mmt.get_min(i):
raise Exception # supposed to happen!
assert 0
except AssertionError:
raise
except Exception:
pass
try:
for i in range(0, MINMAXTABLE_SIZE):
if mmt2.get_max(i) != mmt.get_max(i):
raise Exception # supposed to happen!
assert 0
except AssertionError:
raise
except Exception:
pass
def test_filter_limit_n(self):
ht = khmer.new_hashtable(4, 4**4)
filename = utils.get_test_data('simple_3.fa')
outname = utils.get_temp_filename('test_filter.out')
(total_reads, n_consumed) = ht.consume_fasta(filename)
assert total_reads == 2, total_reads
(total_reads, n_seq_kept) = \
khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
7)
assert total_reads == 2
assert n_seq_kept == 1
(total_reads, n_seq_kept) = \
khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
4)
assert total_reads == 2
assert n_seq_kept == 2
def test_save_load_tagset_trunc():
ht = khmer.new_hashbits(32, 1, 1)
outfile = utils.get_temp_filename('tagset')
ht.add_tag('A' * 32)
ht.add_tag('G' * 32)
ht.save_tagset(outfile)
ht.save_tagset('/tmp/goodversion-k32.tagset')
# truncate tagset file...
fp = open(outfile, 'rb')
data = fp.read()
fp.close()
fp = open(outfile, 'wb')
fp.write(data[:26])
fp.close()
# try loading it...
try:
ht.load_tagset(outfile)
assert 0, "this test should fail"
except IOError:
pass
def test_sweep_reads_3():
infile = utils.get_temp_filename('seqs.fa')
shutil.copyfile(utils.get_test_data('random-20-a.fa'), infile)
wdir = os.path.dirname(infile)
script = scriptpath('sweep-reads.py')
args = ['-m', '75', '-k', '20', '-l', '1', '--prefix',
'test', '--label-by-group', '10', infile, infile]
status, out, err = utils.runscript(script, args, wdir, sandbox=True)
for i in xrange(10):
p = os.path.join(wdir, 'test_{i}.fa'.format(i=i))
print p, err, out
assert os.path.exists(p)
os.remove(p)
counts_fn = os.path.join(wdir, 'test.counts.csv')
with open(counts_fn) as cfp:
for line in cfp:
_, _, c = line.partition(',')
assert int(c) in [9, 10]
assert os.path.exists(counts_fn)
assert os.path.exists(os.path.join(wdir, 'test.dist.txt'))
assert not os.path.exists(os.path.join(wdir, 'test_multi.fa'))
def test_save_load_tagset_trunc():
ht = khmer.new_hashbits(32, 1, 1)
outfile = utils.get_temp_filename('tagset')
ht.add_tag('A' * 32)
ht.add_tag('G' * 32)
ht.save_tagset(outfile)
ht.save_tagset('/tmp/goodversion-k32.tagset')
# truncate tagset file...
fp = open(outfile, 'rb')
data = fp.read()
fp.close()
fp = open(outfile, 'wb')
fp.write(data[:26])
fp.close()
# try loading it...
try:
ht.load_tagset(outfile)
assert 0, "this test should fail"
except IOError:
pass
def test_tiny_real_partitions():
filename = utils.get_test_data('real-partition-tiny.fa')
ht = khmer.new_hashbits(32, 8e1, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
outfile = utils.get_temp_filename('part')
ht.output_partitions(filename, outfile)
data = open(outfile).read()
assert len(data)
records = [r for r in screed.open(outfile)]
names = [r.name for r in records]
parts = [n.rsplit('\t', 1)[1] for n in names]
assert len(parts) == 2, len(parts)
assert len(set(parts)) == 1
assert set(parts) != set(['0'])
test_tiny_real_partitions.runme = True
def test_abundance_dist_single_nobigcount():
infile = utils.get_temp_filename('test.fa')
outfile = utils.get_temp_filename('test.dist')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
script = scriptpath('abundance-dist-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '-b', infile, outfile]
runscript(script, args, in_dir)
fp = iter(open(outfile))
line = fp.next().strip()
assert line == '1 96 96 0.98', line
line = fp.next().strip()
assert line == '255 2 98 1.0', line
def test_abund(self):
ht = khmer.new_hashtable(10, 4**10)
filename = utils.get_test_data('test-abund-read.fa')
outname = utils.get_temp_filename('test_abund.out')
ht.consume_fasta(filename)
try:
ht.consume_fasta()
assert 0, "should fail"
except TypeError as err:
print str(err)
try:
ht.consume_fasta("nonexistent")
assert 0, "should fail"
except IOError as err:
print str(err)
ht.output_fasta_kmer_pos_freq(filename, outname)
try:
ht.output_fasta_kmer_pos_freq()
assert 0, "should fail"
except TypeError as err:
print str(err)
fd = open(outname, "r")
output = fd.readlines()
assert len(output) == 1
output = output[0]
output = output.strip().split()
assert ['1'] * (114 - 10 + 1) == output
fd.close()
def test_abund(self):
ht = khmer.new_hashtable(10, 4 ** 10)
filename = utils.get_test_data('test-abund-read.fa')
outname = utils.get_temp_filename('test_abund.out')
ht.consume_fasta(filename)
try:
ht.consume_fasta()
assert 0, "should fail"
except TypeError as err:
print str(err)
try:
ht.consume_fasta("nonexistent")
assert 0, "should fail"
except IOError as err:
print str(err)
ht.output_fasta_kmer_pos_freq(filename, outname)
try:
ht.output_fasta_kmer_pos_freq()
assert 0, "should fail"
except TypeError as err:
print str(err)
fd = open(outname, "r")
output = fd.readlines()
assert len(output) == 1
output = output[0]
output = output.strip().split()
assert ['1'] * (114 - 10 + 1) == output
fd.close()
def test_feature_extraction_kmer():
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('example.mito.fasta.shreded.subset'),
infile)
outfile = infile + '.kmer_vector'
script = scriptpath('feature_extraction_kmer.py')
mmp = os.path.abspath("../scripts/gm_parameters/par_11.modified")
print mmp
tmp = os.path.abspath("./")
print tmp
print in_dir
args = [
"--input", infile, "--outfile", outfile, "--taxid", "12345", "--label",
"taxid"
]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile), outfile
print outfile
data = [x.strip() for x in open(outfile)]
print len(data)
assert len(data) == 54
assert data[1].startswith("12345\tgi|511782593|ref|NC_021399.1") == True
assert data[0].endswith(
"0.00300180108065\t0.00640384230538\t0.00380228136882") == True
assert data[-1].startswith(
"12345\tgi|511782593|ref|NC_021399.1||pos|304493..309493") == True
assert data[-1].endswith(
"0.00300180108065\t0.00500300180108\t0.00200120072043") == True
utils.cleanup()
def test_feature_extraction_metamark():
infile = utils.get_temp_filename('test.fa')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('example.mito.fasta.shreded.subset'),
infile)
outfile = infile + '.metamark_vector'
script = scriptpath('feature_extraction_metamark.py')
mmp = os.path.abspath("../scripts/gm_parameters/par_11.modified")
print mmp
tmp = os.path.abspath("./")
print tmp
print in_dir
args = [
"--input", infile, "--outfile", outfile, "--tmp", tmp, "--mmp", mmp,
"--taxid", "12345"
]
utils.runscript(script, args, in_dir)
assert os.path.exists(outfile), outfile
print outfile
data = [x.strip() for x in open(outfile)]
print len(data)
assert len(data) == 30
assert data[1].startswith("12345\tgi|511782593|ref|NC_021399.1") == True
assert data[0].endswith("0.018679\t0.016415\t0.016415") == True
assert data[-1].startswith(
"12345\tgi|511782593|ref|NC_021399.1||pos|295582..300582") == True
assert data[-1].endswith("0.023325\t0.019296\t0.021310") == True
utils.cleanup()
def test_save_load_tagset_trunc():
ht = khmer.new_hashbits(32, 1, 1)
outfile = utils.get_temp_filename('tagset')
ht.add_tag('A' * 32)
ht.add_tag('G' * 32)
ht.save_tagset(outfile)
# truncate tagset file...
fp = open(outfile, 'rb')
data = fp.read()
fp.close()
for i in range(len(data)):
fp = open(outfile, 'wb')
fp.write(data[:i])
fp.close()
# try loading it...
try:
ht.load_tagset(outfile)
assert 0, "this test should fail"
except IOError as err:
print str(err), i
def test_filter_limit_n(self):
ht = khmer.new_hashtable(4, 4**4)
filename = utils.get_test_data('simple_3.fa')
outname = utils.get_temp_filename('test_filter.out')
(total_reads, n_consumed) = ht.consume_fasta(filename)
assert total_reads == 2, total_reads
(total_reads, n_seq_kept) = \
khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
7)
assert total_reads == 2
assert n_seq_kept == 1
(total_reads, n_seq_kept) = \
khmer.filter_fasta_file_limit_n(ht, filename,
total_reads,
outname, 2,
4)
assert total_reads == 2
assert n_seq_kept == 2
def test_save_no_load(self):
filename = utils.get_temp_filename('save')
mmt = self.mmt
for i in range(0, MINMAXTABLE_SIZE):
mmt.add_min(i, i)
mmt.add_max(i, MINMAXTABLE_SIZE-i)
mmt.save(filename)
mmt2 = khmer.new_minmax(MINMAXTABLE_SIZE)
# no load!
try:
for i in range(0, MINMAXTABLE_SIZE):
if mmt2.get_min(i) != mmt.get_min(i):
raise Exception # supposed to happen!
assert 0
except AssertionError:
raise
except Exception:
pass
try:
for i in range(0, MINMAXTABLE_SIZE):
if mmt2.get_max(i) != mmt.get_max(i):
raise Exception # supposed to happen!
assert 0
except AssertionError:
raise
except Exception:
pass
def test_tiny_real_partitions():
filename = utils.get_test_data('real-partition-tiny.fa')
ht = khmer.new_hashbits(32, 8e1, 4)
ht.consume_fasta_and_tag(filename)
subset = ht.do_subset_partition(0, 0)
ht.merge_subset(subset)
outfile = utils.get_temp_filename('part')
ht.output_partitions(filename, outfile)
data = open(outfile).read()
assert len(data)
records = [r for r in screed.open(outfile)]
names = [r.name for r in records]
parts = [n.rsplit('\t', 1)[1] for n in names]
assert len(parts) == 2, len(parts)
assert len(set(parts)) == 1
assert set(parts) != set(['0'])
test_tiny_real_partitions.runme = True
def test_save_no_load(self):
filename = utils.get_temp_filename('tst')
rt = self.rt
rt.set(0, True)
rt.set(1, False)
rt.set(2, True)
rt.set(3, False)
rt.set(4, True)
rt.save(filename)
rt2 = khmer.new_readmask(READTABLE_SIZE)
# no load!
try:
for i in range(5):
if rt.get(i) != rt2.get(i):
raise Exception # supposed to happen; no load.
assert 0
except AssertionError:
raise
except Exception:
pass
def test_load_graph():
script = scriptpath('load-graph.py')
args = ['-x', '1e7', '-N', '2', '-k', '20', '-t']
outfile = utils.get_temp_filename('out')
infile = utils.get_test_data('random-20-a.fa')
args.extend([outfile, infile])
(status, out, err) = utils.runscript(script, args)
assert 'Total number of k-mers: 3959' in err, err
ht_file = outfile + '.pt'
assert os.path.exists(ht_file), ht_file
tagset_file = outfile + '.tagset'
assert os.path.exists(tagset_file), tagset_file
ht = khmer.load_hashbits(ht_file)
ht.load_tagset(tagset_file)
# check to make sure we get the expected result for this data set
# upon partitioning (all in one partition). This is kind of a
# roundabout way of checking that load-graph worked :)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
assert x == (1, 0), x
def test_abundance_dist_single_nobigcount():
infile = utils.get_temp_filename('test.fa')
outfile = utils.get_temp_filename('test.dist')
in_dir = os.path.dirname(infile)
shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
script = scriptpath('abundance-dist-single.py')
args = ['-x', '1e7', '-N', '2', '-k', '17', '-z', '-b', infile, outfile]
utils.runscript(script, args, in_dir)
fp = iter(open(outfile))
line = fp.next().strip()
assert line == '1 96 96 0.98', line
line = fp.next().strip()
assert line == '255 2 98 1.0', line
def test_load_graph():
script = scriptpath('load-graph.py')
args = ['-x', '1e7', '-N', '2', '-k', '20']
outfile = utils.get_temp_filename('out')
infile = utils.get_test_data('random-20-a.fa')
args.extend([outfile, infile])
(status, out, err) = runscript(script, args)
assert status == 0
ht_file = outfile + '.ht'
assert os.path.exists(ht_file), ht_file
tagset_file = outfile + '.tagset'
assert os.path.exists(tagset_file), tagset_file
ht = khmer.load_hashbits(ht_file)
ht.load_tagset(tagset_file)
# check to make sure we get the expected result for this data set
# upon partitioning (all in one partition). This is kind of a
# roundabout way of checking that load-graph worked :)
subset = ht.do_subset_partition(0, 0)
x = ht.subset_count_partitions(subset)
assert x == (1, 0), x
def test_sweep_reads_3():
infile = utils.get_temp_filename('seqs.fa')
shutil.copyfile(utils.get_test_data('random-20-a.fa'), infile)
wdir = os.path.dirname(infile)
script = scriptpath('sweep-reads.py')
args = ['-m', '75', '-k', '20', '-l', '1', '--prefix',
'test', '--label-by-group', '10', infile, infile]
status, out, err = utils.runscript(script, args, wdir, sandbox=True)
for i in xrange(10):
p = os.path.join(wdir, 'test_{i}.fa'.format(i=i))
print p, err, out
assert os.path.exists(p)
os.remove(p)
counts_fn = os.path.join(wdir, 'test.counts.csv')
with open(counts_fn) as cfp:
for line in cfp:
_, _, c = line.partition(',')
assert int(c) in [9, 10]
assert os.path.exists(counts_fn)
assert os.path.exists(os.path.join(wdir, 'test.dist.txt'))
assert not os.path.exists(os.path.join(wdir, 'test_multi.fa'))
def _DEBUG_make_graph(infilename,
SIZE=1e7,
N=2,
K=20,
do_partition=False,
annotate_partitions=False,
stop_big_traverse=False):
script = scriptpath('load-graph.py')
args = ['-x', str(SIZE), '-N', str(N), '-k', str(K)]
outfile = utils.get_temp_filename('out')
infile = utils.get_test_data(infilename)
args.extend([outfile, infile])
(status, out, err) = DEBUG_runscript(script, args)
assert status == 0
ht_file = outfile + '.ht'
assert os.path.exists(ht_file), ht_file
tagset_file = outfile + '.tagset'
assert os.path.exists(tagset_file), tagset_file
if do_partition:
print ">>>> DEBUG: Partitioning <<<"
script = scriptpath('partition-graph.py')
args = [outfile]
if stop_big_traverse:
args.insert(0, '--no-big-traverse')
(status, out, err) = DEBUG_runscript(script, args)
print out
print err
assert status == 0
print ">>>> DEBUG: Merging Partitions <<<"
script = scriptpath('merge-partitions.py')
args = [outfile, '-k', str(K)]
(status, out, err) = DEBUG_runscript(script, args)
print out
print err
assert status == 0
final_pmap_file = outfile + '.pmap.merged'
assert os.path.exists(final_pmap_file)
if annotate_partitions:
print ">>>> DEBUG: Annotating Partitions <<<"
script = scriptpath('annotate-partitions.py')
args = ["-k", str(K), outfile, infilename]
in_dir = os.path.dirname(outfile)
(status, out, err) = DEBUG_runscript(script, args, in_dir)
assert status == 0
baseinfile = os.path.basename(infilename)
assert os.path.exists(os.path.join(in_dir, baseinfile + '.part'))
return outfile
def test_check_file_status_kfile():
fn = utils.get_temp_filename('thisfiledoesnotexist')
check_file_status_exited = False
try:
check_input_files(fn, False)
except SystemExit:
check_file_status_exited = True
assert check_file_status_exited
