def test_set_assembly_kmer(self):
'''test _set_assembly_kmer'''
cluster_dir = os.path.join(data_dir, 'cluster_test_set_assembly_kmer')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name', assembly_kmer=42)
self.assertEqual(c.assembly_kmer, 42)
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(os.path.join(data_dir, 'cluster_test_set_assembly_kmer'), 'name')
self.assertEqual(c.assembly_kmer, 5)
clean_cluster_dir(cluster_dir)
def test_full_run_multiple_vars_in_codon(self):
'''Test complete run where there is a codon with a SNP and an indel'''
fasta_in = os.path.join(data_dir,
'cluster_test_full_run_multiple_vars.fa')
tsv_in = os.path.join(data_dir,
'cluster_test_full_run_multiple_vars.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_multiple_vars'
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir, 'cluster_test_full_run_multiple_vars'),
tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=292,
total_reads_bases=20900)
c.run()
expected = [
'presence_absence1\tpresence_absence1\t1\t0\t539\t292\tcluster_name\t96\t96\t96.91\tcluster_name.l15.c30.ctg.1\t1074\t20.4\t0\t.\tp\t.\t0\t.\tMULTIPLE\t25\t26\tGA\t487\t489\tCAT\t27;26;25\tC;A;T\t27;26;25\t.\tGeneric description of presence_absence1',
'presence_absence1\tpresence_absence1\t1\t0\t539\t292\tcluster_name\t96\t96\t96.91\tcluster_name.l15.c30.ctg.1\t1074\t20.4\t0\t.\tp\t.\t0\tA10fs\tFSHIFT\t28\t28\tG\t491\t491\tG\t26\tG\t26\t.\tGeneric description of presence_absence1',
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
def test_full_run_smtls_snp_varonly_gene(self):
'''test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does have variant'''
fasta_in = os.path.join(data_dir,
'cluster_full_run_smtls_snp_varonly_gene.fa')
tsv_in = os.path.join(data_dir,
'cluster_full_run_smtls_snp_varonly_gene.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var'
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene'),
tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=148,
total_reads_bases=13320)
c.run()
# We shouldn't get an extra 'HET' line because we already know about the snp, so
# included in the report of the known snp
expected = [
'ref_gene\tref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.l15.c30.ctg.1\t335\t39.8\t1\tSNP\tp\tI6M\t1\t.\t.\t16\t18\tATG\t135\t137\tATG\t65;64;63\tA;T;G,A\t65;64;32,31\tref_gene:1:1:I6M:.:Description of I6M snp\t.'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
def test_full_run_cluster_test_full_run_smtls_snp_varonly_nonc(self):
'''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample has the var'''
fasta_in = os.path.join(
data_dir, 'cluster_test_full_run_smtls_snp_varonly_nonc.fa')
tsv_in = os.path.join(
data_dir, 'cluster_test_full_run_smtls_snp_varonly_nonc.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding'
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir,
'cluster_test_full_run_smtls_snp_varonly_nonc'),
tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=148,
total_reads_bases=13320)
c.run()
# We shouldn't get an extra 'HET' line because we already know about the snp, so
# included in the report of the known snp
expected = [
'ref_seq\tref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.l15.c30.ctg.1\t335\t39.8\t1\tSNP\tn\tA18G\t1\t.\t.\t18\t18\tG\t137\t137\tG\t63\tG,A\t32,31\tref_seq:0:1:A18G:.:Description of A18G snp\t.'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
def test_full_run_ok_gene_start_mismatch(self):
'''test complete run where gene extended because too different at end for full nucmer match'''
fasta_in = os.path.join(
data_dir, 'cluster_test_full_run_ok_gene_start_mismatch.fa')
tsv_in = os.path.join(
data_dir,
'cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_gene_start_mismatch'
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir,
'cluster_test_full_run_ok_gene_start_mismatch'),
tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=112,
total_reads_bases=1080)
c.run()
expected = [
'gene\tgene\t1\t0\t27\t112\tcluster_name\t96\t96\t100.0\tcluster_name.l6.c30.ctg.1\t362\t27.8\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tGeneric description of gene'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
def test_full_run_smtls_snp_varonly_gene_2(self):
'''test complete run where samtools calls a snp in a variant only gene'''
# _2 because I think test_full_run_smtls_snp_varonly_gene tests the asame functionality.
# ... but let's leave both tests in anyway
fasta_in = os.path.join(
data_dir, 'cluster_full_run_smtls_snp_varonly_gene_2.fa')
tsv_in = os.path.join(data_dir,
'cluster_full_run_smtls_snp_varonly_gene_2.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_full_run_smtls_snp_varonly_gene_2'
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir,
'cluster_full_run_smtls_snp_varonly_gene_2'), tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=148,
total_reads_bases=13320)
c.run()
expected = [
'ref_gene\tref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\tcluster_name.l15.c30.ctg.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t137\t137\tG\t63\tG,A\t32,31\t.\tGeneric description of ref_gene'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
def test_full_run_ok_variants_only_variant_is_present(self):
'''test complete run of cluster on a variants only gene when variant is present'''
fasta_in = os.path.join(data_dir,
'cluster_test_full_run_ok_variants_only.fa')
tsv_in = os.path.join(
data_dir,
'cluster_test_full_run_ok_variants_only.present.metadata.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_variants_only.present'
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only'),
tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=66,
total_reads_bases=3300)
c.run()
expected = [
'variants_only1\tvariants_only1\t1\t1\t27\t66\tcluster_name\t96\t96\t100.0\tcluster_name.l15.c30.ctg.1\t215\t15.3\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tCGC\t65\t67\tCGC\t18;18;19\tC;G;C\t18;18;19\tvariants_only1:1:1:R3S:.:Ref and assembly have wild type\tGeneric description of variants_only1',
'variants_only1\tvariants_only1\t1\t1\t27\t66\tcluster_name\t96\t96\t100.0\tcluster_name.l15.c30.ctg.1\t215\t15.3\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tGCG\t71\t73\tGCG\t17;17;17\tG;C;G\t17;17;17\tvariants_only1:1:1:I5A:.:Ref and reads have variant so report\tGeneric description of variants_only1',
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
def test_full_run_ok_presence_absence(self):
'''test complete run of cluster on a presence absence gene'''
fasta_in = os.path.join(
data_dir, 'cluster_test_full_run_ok_presence_absence.fa')
tsv_in = os.path.join(
data_dir, 'cluster_test_full_run_ok_presence_absence.metadata.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_test_full_run_ok_presence_absence'
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir,
'cluster_test_full_run_ok_presence_absence'), tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=64,
total_reads_bases=3200)
c.run()
expected = [
'presence_absence1\tpresence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.l15.c30.ctg.1\t213\t15.0\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t30\tGCG\t83\t85\tGTG\t22;22;21\tG;T;G\t22;22;21\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1',
'presence_absence1\tpresence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.l15.c30.ctg.1\t213\t15.0\t0\t.\tp\t.\t0\t.\tSYN\t52\t54\tATT\t107\t109\tATC\t31;31;32\tA;T;C\t31;31;32\t.\tGeneric description of presence_absence1',
'presence_absence1\tpresence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.l15.c30.ctg.1\t213\t15.0\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tCGC\t62\t64\tCGC\t18;17;17\tC;G;C\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1',
'presence_absence1\tpresence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.l15.c30.ctg.1\t213\t15.0\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tGCG\t68\t70\tGCG\t18;20;20\tG;C;G\t18;20;20\tpresence_absence1:1:0:I5A:.:Ref and reads have variant so report\tGeneric description of presence_absence1',
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
def test_full_run_ok_non_coding(self):
'''test complete run of cluster on a noncoding sequence'''
fasta_in = os.path.join(data_dir,
'cluster_test_full_run_ok_non_coding.fa')
tsv_in = os.path.join(
data_dir, 'cluster_test_full_run_ok_non_coding.metadata.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.test_full_run_ok_non_coding'
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir, 'cluster_test_full_run_ok_non_coding'),
tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=72,
total_reads_bases=3600)
c.run()
self.maxDiff = None
expected = [
'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.l15.c30.ctg.1\t234\t15.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t14\t14\tA\t74\t74\tT\t19\tT\t19\tnoncoding1:0:0:A14T:.:ref has wild type, reads has variant so should report\tgeneric description of noncoding1',
'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.l15.c30.ctg.1\t234\t15.4\t0\t.\tn\t.\t0\tG61T\tSNP\t61\t61\tG\t121\t121\tT\t24\tT\t24\t.\tgeneric description of noncoding1',
'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.l15.c30.ctg.1\t234\t15.4\t0\t.\tn\t.\t0\t.82C\tINS\t82\t82\tA\t143\t143\tC\t23\tC\t23\t.\tgeneric description of noncoding1',
'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.l15.c30.ctg.1\t234\t15.4\t0\t.\tn\t.\t0\tT108.\tDEL\t108\t108\tT\t168\t168\tC\t17\tC\t17\t.\tgeneric description of noncoding1',
'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.l15.c30.ctg.1\t234\t15.4\t1\tSNP\tn\tA6G\t1\t.\t.\t6\t6\tG\t66\t66\tG\t19\tG\t19\tnoncoding1:0:0:A6G:.:variant in ref and reads so should report\tgeneric description of noncoding1',
'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.l15.c30.ctg.1\t234\t15.4\t1\tSNP\tn\tG9T\t0\t.\t.\t9\t9\tG\t69\t69\tG\t19\tG\t19\tnoncoding1:0:0:G9T:.:wild type in ref and reads\tgeneric description of noncoding1'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
def test_get_read_counts(self):
'''test _get_read_counts pass'''
cluster_dir = os.path.join(data_dir, 'cluster_test_get_read_counts')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
self.assertEqual(2, c._get_read_counts())
clean_cluster_dir(cluster_dir)
def test_get_mummer_variants(self):
'''test _get_mummer_variants'''
cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
snp_file = os.path.join(data_dir, 'cluster_test_get_mummer_variants.none.snps')
shutil.copyfile(snp_file, c.assembly_vs_gene_coords + '.snps')
c._get_mummer_variants()
self.assertEqual(c.mummer_variants, {})
clean_cluster_dir(cluster_dir)
snp_file = os.path.join(data_dir, 'cluster_test_get_mummer_variants.snp.snps')
shutil.copyfile(snp_file, c.assembly_vs_gene_coords + '.snps')
v1 = pymummer.variant.Variant(pymummer.snp.Snp('42\tA\tG\t42\t42\t42\t500\t500\t1\t1\tgene\tcontig1'))
v2 = pymummer.variant.Variant(pymummer.snp.Snp('42\tA\tG\t42\t42\t42\t500\t500\t1\t1\tgene\tcontig2'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('40\tT\tC\t40\t42\t42\t500\t500\t1\t1\tgene\tcontig1'))
v4 = pymummer.variant.Variant(pymummer.snp.Snp('2\tC\tG\t2\t42\t42\t500\t500\t1\t1\tgene\tcontig1'))
expected = {
'contig1': [[v4], [v3, v1]],
'contig2': [[v2]]
}
shutil.copyfile(snp_file, c.assembly_vs_gene_coords + '.snps')
c._get_mummer_variants()
self.assertEqual(c.mummer_variants, expected)
clean_cluster_dir(cluster_dir)
def test_full_run_ref_not_in_cluster(self):
'''test complete run of cluster when nearest ref is outside cluster'''
fasta_in = os.path.join(
data_dir, 'cluster_test_full_run_ref_not_in_cluster.in.fa')
tsv_in = os.path.join(
data_dir, 'cluster_test_full_run_ref_not_in_cluster.in.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.test_full_run_ref_not_in_cluster'
all_refs_fa = os.path.join(
data_dir, 'cluster_test_full_run_ref_not_in_cluster.all_refs.fa')
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir, 'cluster_test_full_run_ref_not_in_cluster'),
tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=72,
total_reads_bases=3600,
all_ref_seqs_fasta=all_refs_fa)
c.run()
expected = '\t'.join(
['.', '.', '.', '.', '1024', '72', 'cluster_name'] + ['.'] * 24)
self.assertEqual([expected], c.report_lines)
self.assertTrue(c.status_flag.has('ref_seq_choose_fail'))
self.assertFalse(c.status_flag.has('assembly_fail'))
shutil.rmtree(tmpdir)
def test_gene_covered_by_complete_contig_with_orf(self):
'''test _gene_covered_by_complete_contig_with_orf'''
cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
gene = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA')
gene_no_orf = pyfastaq.sequences.Fasta('gene', 'GATTGAGAAGCGATGACCCATGAAGCGACCGAACGCTGA')
c.gene = gene
hit1 = ['1', '39', '1', '39', '39', '39', '100.00', '39', '39', '1', '1', 'gene', 'contig1']
hit2 = ['1', '20', '1', '20', '20', '20', '100.00', '39', '39', '1', '1', 'gene', 'contig1']
hit3 = ['21', '39', '21', '39', '19', '19', '100.00', '39', '39', '1', '1', 'gene', 'contig2']
nucmer_hits = [
{'contig1': [pymummer.alignment.Alignment('\t'.join(hit1))]},
{'contig1': [pymummer.alignment.Alignment('\t'.join(hit1))]},
{'contig2': [pymummer.alignment.Alignment('\t'.join(hit2))]},
{'contig2': [pymummer.alignment.Alignment('\t'.join(hit2)), pymummer.alignment.Alignment('\t'.join(hit3))]},
]
expected = [True, False, False, False]
assemblies = [
{'contig1': gene},
{'contig1': gene_no_orf},
{'contig1': gene},
{'contig1': gene, 'contig2': pyfastaq.sequences.Fasta('contig2', 'ACGT')}
]
assert len(expected) == len(nucmer_hits) == len(assemblies)
for i in range(len(expected)):
c.final_assembly = assemblies[i]
c.nucmer_hits = nucmer_hits[i]
self.assertEqual(c._gene_covered_by_complete_contig_with_orf(), expected[i])
clean_cluster_dir(cluster_dir)
def test_get_samtools_variants(self):
'''test _get_samtools_variants'''
cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
c.final_assembly_vcf = os.path.join(data_dir, 'cluster_test_get_samtools_variants.vcf')
c.final_assembly_read_depths = os.path.join(data_dir, 'cluster_test_get_samtools_variants.read_depths.gz')
positions = [
('16__cat_2_M35190.scaffold.1', 92),
('16__cat_2_M35190.scaffold.1', 179),
('16__cat_2_M35190.scaffold.1', 263),
('16__cat_2_M35190.scaffold.6', 93)
]
expected = {
'16__cat_2_M35190.scaffold.1': {
92: ('T', 'A', 123, '65,58'),
179: ('A', 'T', 86, '41,45'),
263: ('G', 'C', 97, '53,44'),
},
'16__cat_2_M35190.scaffold.6': {
93: ('T', 'G', 99, '56,43')
}
}
got = c._get_samtools_variants(positions)
self.assertEqual(expected, got)
def test_nucmer_hits_to_ref_coords(self):
'''test _nucmer_hits_to_ref_coords'''
cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
hits = [
['1', '42', '1', '42', '42', '42', '100.00', '1000', '1000', '1', '1', 'gene', 'contig1'],
['100', '142', '200', '242', '42', '42', '99.42', '1000', '1000', '1', '1', 'gene', 'contig1'],
['100', '110', '200', '210', '11', '11', '99.42', '1000', '1000', '1', '1', 'gene', 'contig2'],
]
c.nucmer_hits = {
'contig1': [
pymummer.alignment.Alignment('\t'.join(hits[0])),
pymummer.alignment.Alignment('\t'.join(hits[1])),
],
'contig2': [
pymummer.alignment.Alignment('\t'.join(hits[2])),
]
}
got_coords = c._nucmer_hits_to_ref_coords()
expected = [
pyfastaq.intervals.Interval(0,41),
pyfastaq.intervals.Interval(99, 109),
pyfastaq.intervals.Interval(99, 141),
]
self.assertEqual(got_coords, expected)
got_coords = c._nucmer_hits_to_ref_coords(contig='contig2')
expected = [
pyfastaq.intervals.Interval(99, 109),
]
self.assertEqual(got_coords, expected)
clean_cluster_dir(cluster_dir)
def test_nucmer_hits_to_scaff_coords(self):
'''test _nucmer_hits_to_scaff_coords'''
cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
hits = [
['1', '10', '1', '10', '10', '10', '100.00', '1000', '1000', '1', '1', 'gene', 'scaff1'],
['9', '42', '9', '42', '34', '34', '100.00', '1000', '1000', '1', '1', 'gene', 'scaff1'],
['50', '52', '50', '52', '3', '3', '100.00', '1000', '1000', '1', '1', 'gene', 'scaff1'],
['1', '42', '1', '42', '42', '42', '100.00', '1000', '1000', '1', '1', 'gene', 'scaff2'],
]
c.nucmer_hits = {
'scaff1': [
pymummer.alignment.Alignment('\t'.join(hits[0])),
pymummer.alignment.Alignment('\t'.join(hits[1])),
pymummer.alignment.Alignment('\t'.join(hits[2])),
],
'scaff2': [
pymummer.alignment.Alignment('\t'.join(hits[3])),
]
}
got = c._nucmer_hits_to_scaff_coords()
expected = {
'scaff1': [
pyfastaq.intervals.Interval(0, 41),
pyfastaq.intervals.Interval(49, 51)
],
'scaff2': [
pyfastaq.intervals.Interval(0, 41),
]
}
self.assertEqual(got, expected)
clean_cluster_dir(cluster_dir)
def test_full_run_assembly_fail(self):
'''test complete run of cluster when assembly fails'''
fasta_in = os.path.join(data_dir,
'cluster_test_full_run_assembly_fail.in.fa')
tsv_in = os.path.join(data_dir,
'cluster_test_full_run_assembly_fail.in.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.test_full_run_assembly_fail'
shutil.rmtree(tmpdir, ignore_errors=True)
shutil.copytree(
os.path.join(data_dir, 'cluster_test_full_run_assembly_fail'),
tmpdir)
c = cluster.Cluster(tmpdir,
'cluster_name',
refdata,
total_reads=4,
total_reads_bases=304)
c.run()
expected = '\t'.join(['.', '.', '.', '.', '64', '4', 'cluster_name'] +
['.'] * 24)
self.assertEqual([expected], c.report_lines)
self.assertFalse(c.status_flag.has('ref_seq_choose_fail'))
self.assertTrue(c.status_flag.has('assembly_fail'))
shutil.rmtree(tmpdir)
def test_get_read_counts_fail(self):
'''test _get_read_counts fail'''
cluster_dir = os.path.join(data_dir, 'cluster_test_get_read_counts_fail')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
with self.assertRaises(cluster.Error):
c._get_read_counts()
clean_cluster_dir(cluster_dir)
def test_get_best_gene_by_alignment_score(self):
'''test _get_best_gene_by_alignment_score'''
cluster_dir = os.path.join(data_dir, 'cluster_test_get_best_gene_by_alignment_score')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
got_name = c._get_best_gene_by_alignment_score()
self.assertEqual(got_name, '1')
clean_cluster_dir(cluster_dir)
def test_assemble_with_spades_fail(self):
'''test _assemble_with_spades handles spades fail'''
cluster_dir = os.path.join(data_dir, 'cluster_test_assemble_with_spades')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
shutil.copyfile(os.path.join(data_dir, 'cluster_test_assemble_with_spades.gene.fa'), c.gene_fa)
c._assemble_with_spades()
self.assertEqual(c.status_flag.to_number(), 64)
clean_cluster_dir(cluster_dir)
def test_get_total_alignment_score(self):
'''test _get_total_alignment_score'''
cluster_dir = os.path.join(data_dir, 'cluster_test_get_total_alignment_score')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
got_score = c._get_total_alignment_score('1')
expected_score = 3000
self.assertEqual(got_score, expected_score)
clean_cluster_dir(cluster_dir)
def test_gene_coverage_unique(self):
'''test _gene_coverage_unique'''
cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
c.gene = pyfastaq.sequences.Fasta('gene', 'ACGTGTGCAT')
hit1 = ['1', '10', '1', '10', '10', '10', '100.00', '10', '10', '1', '1', 'gene', 'contig1']
hit2 = ['1', '5', '1', '5', '5', '5', '100.00', '10', '10', '1', '1', 'gene', 'contig2']
c.nucmer_hits = { 'contig1': [pymummer.alignment.Alignment('\t'.join(hit1))] }
self.assertTrue(c._gene_coverage_unique())
c.nucmer_hits['contig2'] = [pymummer.alignment.Alignment('\t'.join(hit2))]
self.assertFalse(c._gene_coverage_unique())
def test_fix_contig_orientation(self):
'''test _fix_contig_orientation'''
cluster_dir = os.path.join(data_dir, 'cluster_test_fix_contig_orientation')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
scaffs_in = os.path.join(data_dir, 'cluster_test_fix_contig_orientation.in.fa')
scaffs_out = os.path.join(data_dir, 'cluster_test_fix_contig_orientation.out.fa')
shutil.copyfile(scaffs_in, c.gapfilled_scaffolds)
shutil.copyfile(os.path.join(data_dir, 'cluster_test_fix_contig_orientation.gene.fa'), c.gene_fa)
c._fix_contig_orientation()
self.assertTrue(filecmp.cmp(scaffs_out, c.final_assembly_fa, shallow=False))
clean_cluster_dir(cluster_dir)
def test_scaffold_with_sspace(self):
'''test _scaffold_with_sspace'''
cluster_dir = os.path.join(data_dir, 'cluster_test_scaffold_with_sspace')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
shutil.copyfile(
os.path.join(data_dir, 'cluster_test_scaffold_with_sspace.contigs.fa'),
c.assembly_contigs
)
#shutil.copyfile(os.path.join(data_dir, 'cluster_test_scaffold_with_sspace.gene.fa'), c.gene_fa)
c._scaffold_with_sspace()
self.assertTrue(os.path.exists(c.scaffolder_scaffolds))
clean_cluster_dir(cluster_dir)
def test_gap_fill_with_gapfiller_with_gaps(self):
'''test _gap_fill_with_gapfiller with gaps'''
cluster_dir = os.path.join(data_dir, 'cluster_test_gapfill_with_gapfiller')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
shutil.copyfile(
os.path.join(data_dir, 'cluster_test_gapfill_with_gapfiller.scaffolds_with_gaps.fa'),
c.scaffolder_scaffolds
)
c.gene = pyfastaq.sequences.Fasta('name_of_gene', 'AAACCCGGGTTT')
c._gap_fill_with_gapfiller()
self.assertTrue(os.path.exists(c.gapfilled_scaffolds))
clean_cluster_dir(cluster_dir)
def test_rename_scaffolds(self):
'''test _rename_scaffolds'''
cluster_dir = os.path.join(data_dir, 'cluster_test_rename_scaffolds')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
c.gene = pyfastaq.sequences.Fasta('name_of_gene', 'AAACCCGGGTTT')
infile = os.path.join(data_dir, 'cluster_test_rename_scaffolds.in.fa')
outfile = os.path.join(data_dir, 'cluster_test_rename_scaffolds.out.fa')
tmpfile = 'tmp.fa'
c._rename_scaffolds(infile, tmpfile)
self.assertTrue(filecmp.cmp(outfile, tmpfile, shallow=False))
os.unlink(tmpfile)
clean_cluster_dir(cluster_dir)
def test_get_samtools_variant_positions(self):
'''test _get_samtools_variant_positions'''
cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
c.final_assembly_vcf = os.path.join(data_dir, 'cluster_test_get_samtools_variant_positions.vcf')
expected = [
('16__cat_2_M35190.scaffold.1', 92),
('16__cat_2_M35190.scaffold.1', 179),
('16__cat_2_M35190.scaffold.1', 263),
('16__cat_2_M35190.scaffold.6', 93)
]
self.assertEqual(expected, c._get_samtools_variant_positions())
def test_full_run_smtls_snp_varonly_nonc(self):
'''test complete run where samtools calls a snp in a presence/absence noncoding sequence'''
fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc.fa')
tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc.tsv')
refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
tmpdir = 'tmp.cluster_full_run_smtls_snp_varonly_nonc'
shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc'), tmpdir)
c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320)
c.run()
expected = [
'ref_seq\tref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\tcluster_name.l15.c30.ctg.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t137\t137\tG\t63\tG,A\t32,31\t.\tGeneric description of ref_seq'
]
self.assertEqual(expected, c.report_lines)
shutil.rmtree(tmpdir)
def test_init_fail_files_missing(self):
'''test init_fail_files_missing'''
dirs = [
'cluster_test_directorynotexist'
'cluster_test_init_no_genes_fa',
'cluster_test_init_no_reads_1',
'cluster_test_init_no_reads_2',
]
dirs = [os.path.join(data_dir, d) for d in dirs]
for d in dirs:
clean_cluster_dir(d)
with self.assertRaises(cluster.Error):
c = cluster.Cluster(d, 'name')
clean_cluster_dir(d)
def test_filter_mummer_variants(self):
'''test filter_mummer_variants'''
cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
clean_cluster_dir(cluster_dir)
c = cluster.Cluster(cluster_dir, 'name')
c.gene = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA')
v1 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v2 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('12\tG\tT\t12\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
c.mummer_variants = {'contig': [[v1, v2], v3]}
c._filter_mummer_variants()
expected = {'contig': [[v1, v2]]}
self.assertEqual(expected, c.mummer_variants)
clean_cluster_dir(cluster_dir)
