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Make cdhit optional #29

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Jun 10, 2015
Merged

Make cdhit optional #29

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a5b8cab
Add method to fake run cd-hit
Jun 10, 2015
fd65668
Add option to skip cd-hit
Jun 10, 2015
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23 changes: 21 additions & 2 deletions ariba/cdhit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,25 @@ def __init__(
self.verbose = verbose


def fake_run(self):
'''Doesn't actually run cd-hit. Instead, puts each input sequence into its own cluster. So it's as if cdhit was run, but didn't cluster anything'''
cluster_to_name = {}
found_names = set()
seq_reader = pyfastaq.sequences.file_reader(self.infile)
f = pyfastaq.utils.open_file_write(self.outfile)
for seq in seq_reader:
if seq.id in found_names:
raise Error('Sequence name "' + seq.id + '" not unique. Cannot continue')
found_names.add(seq.id)
cluster_number = str(len(cluster_to_name))
cluster_to_name[cluster_number] = {seq.id}
seq.id = cluster_number
print(seq, file=f)

pyfastaq.utils.close(f)
return cluster_to_name


def run(self):
tmpdir = tempfile.mkdtemp(prefix='tmp.run_cd-hit.', dir=os.getcwd())
cdhit_fasta = os.path.join(tmpdir, 'cdhit')
Expand All @@ -51,7 +70,7 @@ def run(self):
'-bak 1',
])

common.syscall(cmd, verbose=self.verbose)
common.syscall(cmd, verbose=self.verbose)

cluster_representatives = self._get_ids(cdhit_fasta)
clusters, cluster_rep_to_cluster = self._parse_cluster_info_file(cluster_info_outfile, new_to_old_name, cluster_representatives)
Expand All @@ -64,7 +83,7 @@ def _enumerate_fasta(self, infile, outfile):
rename_file = outfile + '.tmp.rename_info'
assert not os.path.exists(rename_file)
pyfastaq.tasks.enumerate_names(infile, outfile, rename_file=rename_file)

with open(rename_file) as f:
lines = [x.rstrip().split('\t') for x in f.readlines() if x != '#old\tnew\n']
new_to_old_name = {x[1]: x[0] for x in lines}
Expand Down
15 changes: 11 additions & 4 deletions ariba/clusters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@ def __init__(self,
velvet_exe='velvet', # prefix of velvet{g,h}
cdhit_seq_identity_threshold=0.9,
cdhit_length_diff_cutoff=0.9,
run_cd_hit=True,
clean=1,
):
self.db_fasta = os.path.abspath(db_fasta)
Expand Down Expand Up @@ -111,6 +112,7 @@ def __init__(self,

self.cdhit_seq_identity_threshold = cdhit_seq_identity_threshold
self.cdhit_length_diff_cutoff = cdhit_length_diff_cutoff
self.run_cd_hit = run_cd_hit

for d in [self.outdir, self.clusters_outdir]:
try:
Expand All @@ -121,13 +123,18 @@ def __init__(self,
def _run_cdhit(self):
r = cdhit.Runner(
self.db_fasta,
self.db_fasta_clustered,
self.db_fasta_clustered,
seq_identity_threshold=self.cdhit_seq_identity_threshold,
threads=self.threads,
length_diff_cutoff=self.cdhit_length_diff_cutoff,
verbose=self.verbose,
)
self.cluster_ids = r.run()
if self.run_cd_hit:
self.cluster_ids = r.run()
else:
if self.verbose:
print('Skipping cd-hit because --no_cdhit option used')
self.cluster_ids = r.fake_run()


def _write_clusters_info_file(self):
Expand Down Expand Up @@ -338,7 +345,7 @@ def _write_reports(self):

columns[0] = 'gene'
workbook = openpyxl.Workbook()
worksheet = workbook.worksheets[0]
worksheet = workbook.worksheets[0]
worksheet.title = 'ARIBA_report'
worksheet.append(columns)

Expand Down Expand Up @@ -383,7 +390,7 @@ def run(self):

if self.verbose:
print('{:_^79}'.format(' Running cd-hit '), flush=True)
self._run_cdhit()
self._run_cdhit()
self._write_clusters_info_file()
if self.verbose:
print('Finished cd-hit\n')
Expand Down
2 changes: 2 additions & 0 deletions ariba/tasks/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ def run():
parser.add_argument('outdir', help='Output directory (must not already exist)')

cdhit_group = parser.add_argument_group('cd-hit options')
cdhit_group.add_argument('--no_cdhit', action='store_true', help='Do not run cd-hit')
cdhit_group.add_argument('--cdhit_seq_identity_threshold', type=float, help='Sequence identity threshold (cd-hit option -c) [%(default)s]', default=0.9, metavar='FLOAT')
cdhit_group.add_argument('--cdhit_length_diff_cutoff', type=float, help='length difference cutoff (cd-hit option -s) [%(default)s]', default=0.9, metavar='FLOAT')

Expand Down Expand Up @@ -84,6 +85,7 @@ def run():
cdhit_seq_identity_threshold=options.cdhit_seq_identity_threshold,
cdhit_length_diff_cutoff=options.cdhit_length_diff_cutoff,
clean=options.clean,
run_cd_hit=(not options.no_cdhit)
)
c.run()

29 changes: 29 additions & 0 deletions ariba/tests/cdhit_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,3 +78,32 @@ def test_run(self):
self.assertEqual(clusters, expected_clusters)
self.assertTrue(filecmp.cmp(tmpfile, expected_outfile, shallow=False))
os.unlink(tmpfile)


def test_fake_run(self):
'''test fake_run'''
infile = os.path.join(data_dir, 'cdhit_test_fake_run.in.fa')
expected_outfile = os.path.join(data_dir, 'cdhit_test_fake_run.out.fa')
tmpfile = 'tmp.cdhit_test_fake_run.out.fa'
r = cdhit.Runner(infile, tmpfile)
clusters = r.fake_run()
expected_clusters = {
'0': {'seq1'},
'1': {'seq2'},
'2': {'seq3'},
'3': {'seq4'},
}
self.assertEqual(clusters, expected_clusters)
self.assertTrue(filecmp.cmp(tmpfile, expected_outfile, shallow=False))
os.unlink(tmpfile)


def test_fake_run_fail(self):
'''test fake_run with non-unique names'''
infile = os.path.join(data_dir, 'cdhit_test_fake_run.non-unique.in.fa')
tmpfile = 'tmp.cdhit_test_fake_run.out.non-unique.fa'
r = cdhit.Runner(infile, tmpfile)
with self.assertRaises(cdhit.Error):
clusters = r.fake_run()
os.unlink(tmpfile)

40 changes: 40 additions & 0 deletions ariba/tests/data/cdhit_test_fake_run.in.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
>seq1
TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA
GGAGGTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG
AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC
TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG
AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC
ACGGTGAATAGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA
GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA
TACACTCACGTAGGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA
AACTCTATCGTAGGGTCGCA
>seq2
TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA
GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG
AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC
TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG
AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC
ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA
GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA
TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA
AACTCTATGTAGGGTCGCA
>seq3
TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGTTCTATGCAGGCTTGTGAA
GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG
AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAGGCCATACACTTAGCTCA
TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG
AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGATAGCC
ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA
GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA
TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGATGCGAATTGAAACAA
AACTCTATGTAGGGTCGCA
>seq4
CAAGGGCGGATTCGAACGGGTAACAGGGATCTGATTGGCTCCGGCCAGCTGGTGGATATC
TGCATCCGTTGACCCACCAACTTTAGCAGTATAGACCCTAAACTGGCATGGTGCCCTTTT
TATATCCCGATGCATCTGGAGAAACCGTCAGGACCTCTTAAGCCCCGTGGAGAGCCAAAC
TTCCAACCACGTCAAGGCAACCTTGGTTTAGCACAGGGCTCCCAGTGGGTGTAAGGGATG
AACACTACCCGGCCCACCGTCGATTTAGCCCTAAATGGTCTATTGCTCACGGGTAGCACA
CAAGTAATAAAAACGTATTCAGCTCGAGTCAGCGTCCAGCCATTTTACTTTGCGTCATCG
AGGGGTAGTGCCTCCGAGAATCAAGGTTTGATTATACTAAACGGAGGGGCCTACCACTCA
GCCAGTCTTTGCATCGTCCATTCCCGCCGTTTATGGGTCACTATTCATTCGGAATTTGGA
TGCGGTCAACAAGTCCAGGT
40 changes: 40 additions & 0 deletions ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
>seq1
TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA
GGAGGTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG
AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC
TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG
AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC
ACGGTGAATAGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA
GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA
TACACTCACGTAGGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA
AACTCTATCGTAGGGTCGCA
>seq2
TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA
GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG
AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC
TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG
AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC
ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA
GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA
TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA
AACTCTATGTAGGGTCGCA
>seq1
TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGTTCTATGCAGGCTTGTGAA
GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG
AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAGGCCATACACTTAGCTCA
TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG
AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGATAGCC
ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA
GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA
TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGATGCGAATTGAAACAA
AACTCTATGTAGGGTCGCA
>seq4
CAAGGGCGGATTCGAACGGGTAACAGGGATCTGATTGGCTCCGGCCAGCTGGTGGATATC
TGCATCCGTTGACCCACCAACTTTAGCAGTATAGACCCTAAACTGGCATGGTGCCCTTTT
TATATCCCGATGCATCTGGAGAAACCGTCAGGACCTCTTAAGCCCCGTGGAGAGCCAAAC
TTCCAACCACGTCAAGGCAACCTTGGTTTAGCACAGGGCTCCCAGTGGGTGTAAGGGATG
AACACTACCCGGCCCACCGTCGATTTAGCCCTAAATGGTCTATTGCTCACGGGTAGCACA
CAAGTAATAAAAACGTATTCAGCTCGAGTCAGCGTCCAGCCATTTTACTTTGCGTCATCG
AGGGGTAGTGCCTCCGAGAATCAAGGTTTGATTATACTAAACGGAGGGGCCTACCACTCA
GCCAGTCTTTGCATCGTCCATTCCCGCCGTTTATGGGTCACTATTCATTCGGAATTTGGA
TGCGGTCAACAAGTCCAGGT
40 changes: 40 additions & 0 deletions ariba/tests/data/cdhit_test_fake_run.out.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
>0
TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA
GGAGGTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG
AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC
TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG
AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC
ACGGTGAATAGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA
GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA
TACACTCACGTAGGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA
AACTCTATCGTAGGGTCGCA
>1
TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGCCCTATGCAGGCTTGTGAA
GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG
AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAAGGCCATACACTTAGCTC
TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG
AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGACAGCC
ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA
GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA
TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGTTGCGAATTGAAACAA
AACTCTATGTAGGGTCGCA
>2
TGGGGAATATAGTGGGTACTGTGTGTTGAGCGATTCCCGAGTTCTATGCAGGCTTGTGAA
GGAGTTCGTGGGATGCTCGTGTCTTCACGAACTTAAAGCCCCTCTTTGGCTTAGGGCCGG
AGATCGCGTCATAAGTGTAATCTAGCGTTGCAGGTATGGGTAGGCCATACACTTAGCTCA
TGATGTGATGTGTCAGGTCTGGAGTTTACATATGTCCTGCCACGGTCCTATTTGTTAGAG
AGGCCTTCAGGCGGCCCCTGCCCGTCGATTCGGCAAACTGCCGAAAACGGAGAGATAGCC
ACGGTGAATGGAATCTTGGCATACGGTTAATCAGTGCTCTGCTAGTCCTGCTTTCTCTAA
GCTTATAGAATTCCTGATATATTAAGTAACTTTTCCATTCCATAGACGCGACGAACTGGA
TACACTCACGTATGCTCGATCATGAAAGTGAAAGGCGCTCCAAGATGCGAATTGAAACAA
AACTCTATGTAGGGTCGCA
>3
CAAGGGCGGATTCGAACGGGTAACAGGGATCTGATTGGCTCCGGCCAGCTGGTGGATATC
TGCATCCGTTGACCCACCAACTTTAGCAGTATAGACCCTAAACTGGCATGGTGCCCTTTT
TATATCCCGATGCATCTGGAGAAACCGTCAGGACCTCTTAAGCCCCGTGGAGAGCCAAAC
TTCCAACCACGTCAAGGCAACCTTGGTTTAGCACAGGGCTCCCAGTGGGTGTAAGGGATG
AACACTACCCGGCCCACCGTCGATTTAGCCCTAAATGGTCTATTGCTCACGGGTAGCACA
CAAGTAATAAAAACGTATTCAGCTCGAGTCAGCGTCCAGCCATTTTACTTTGCGTCATCG
AGGGGTAGTGCCTCCGAGAATCAAGGTTTGATTATACTAAACGGAGGGGCCTACCACTCA
GCCAGTCTTTGCATCGTCCATTCCCGCCGTTTATGGGTCACTATTCATTCGGAATTTGGA
TGCGGTCAACAAGTCCAGGT