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Changed x's to upper case to see if this fixes the Docker build
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@kpepper
kpepper committed Mar 13, 2019
1 parent 57430c7 commit bb118b3
Showing 1 changed file with 44 additions and 44 deletions.
88 changes: 44 additions & 44 deletions ariba/tests/assembly_variants_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,23 +52,23 @@ def test_get_mummer_variants_has_variants(self):
def test_get_variant_effect(self):
'''test _get_variant_effect'''
ref_seq = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA')
v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v2 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v4 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v5 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v2 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tA\t6\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v4 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tA\t6\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v5 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v7.qry_base = 'GAT'
v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v8.qry_base = 'TGA'
v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tG\t4\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v9.qry_base = 'ATTCCT'
v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v10.ref_base = 'CGC'
v10.ref_end = 5
v11 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
v11 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\t.\t4\tX\tX\t39\t39\tX\tX\tgene\tcontig'))
v11.ref_base = 'CGCGAA'
v11.ref_end = 8

Expand All @@ -93,9 +93,9 @@ def test_get_variant_effect(self):
def test_filter_mummer_variants(self):
'''test filter_mummer_variants'''
ref_seq = 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'))
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'))
mummer_variants = {'contig': [[v1, v2], v3]}
assembly_variants.AssemblyVariants._filter_mummer_variants(mummer_variants, ref_seq)
expected = {'contig': [[v1, v2]]}
Expand All @@ -110,13 +110,13 @@ def test_one_var_one_ctg_noncdg(self):
ref_sequence_name = 'non_coding'
refdata_var_dict = refdata.metadata[ref_sequence_name]

v0 = pymummer.variant.Variant(pymummer.snp.Snp('2\tT\tA\t2\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))
v0 = pymummer.variant.Variant(pymummer.snp.Snp('2\tT\tA\t2\tX\tX\t42\t42\tX\tX\tnon_coding\tcontig'))

# ref has A at position 3, which is variant type. This gives contig the wild type C. Shouldn't report
v1 = pymummer.variant.Variant(pymummer.snp.Snp('3\tA\tC\t3\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))
v1 = pymummer.variant.Variant(pymummer.snp.Snp('3\tA\tC\t3\tX\tX\t42\t42\tX\tX\tnon_coding\tcontig'))

# ref has T at position 5, which is wild type. This gives contig variant type A. Should report
v2 = pymummer.variant.Variant(pymummer.snp.Snp('5\tT\tA\t5\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))
v2 = pymummer.variant.Variant(pymummer.snp.Snp('5\tT\tA\t5\tX\tX\t42\t42\tX\tX\tnon_coding\tcontig'))

meta0 = sequence_metadata.SequenceMetadata('non_coding\t0\t0\tC3A\tid1\tref has variant type A')
meta2 = sequence_metadata.SequenceMetadata('non_coding\t0\t0\tT5A\tid1\tref has wild type T')
Expand Down Expand Up @@ -153,33 +153,33 @@ def test_one_var_one_ctg_cdg(self):
ref_sequence = refdata.sequence(ref_sequence_name)
refdata_var_dict = refdata.metadata[ref_sequence_name]

v0 = pymummer.variant.Variant(pymummer.snp.Snp('6\tT\tA\t6\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
v1 = pymummer.variant.Variant(pymummer.snp.Snp('9\tA\tT\t9\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
v2 = pymummer.variant.Variant(pymummer.snp.Snp('18\tG\tT\t18\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('21\tC\tT\t21\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
v4 = pymummer.variant.Variant(pymummer.snp.Snp('7\tA\tT\t7\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
v5 = pymummer.variant.Variant(pymummer.snp.Snp('12\tA\tC\t11\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
v0 = pymummer.variant.Variant(pymummer.snp.Snp('6\tT\tA\t6\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
v1 = pymummer.variant.Variant(pymummer.snp.Snp('9\tA\tT\t9\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
v2 = pymummer.variant.Variant(pymummer.snp.Snp('18\tG\tT\t18\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('21\tC\tT\t21\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
v4 = pymummer.variant.Variant(pymummer.snp.Snp('7\tA\tT\t7\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
v5 = pymummer.variant.Variant(pymummer.snp.Snp('12\tA\tC\t11\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))

v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
self.assertTrue(v6.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
v6 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
self.assertTrue(v6.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))

v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
self.assertTrue(v7.update_indel(pymummer.snp.Snp('4\t.\tA\t5\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
v7 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
self.assertTrue(v7.update_indel(pymummer.snp.Snp('4\t.\tA\t5\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))

v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
self.assertTrue(v8.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
self.assertTrue(v8.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
v8 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
self.assertTrue(v8.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))
self.assertTrue(v8.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))

v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('7\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('8\tG\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('9\tA\t.\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
v9 = pymummer.variant.Variant(pymummer.snp.Snp('4\tG\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('5\tA\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('6\tT\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('7\tA\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('8\tG\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))
self.assertTrue(v9.update_indel(pymummer.snp.Snp('9\tA\t.\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))

v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t5\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t6\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')))
v10 = pymummer.variant.Variant(pymummer.snp.Snp('4\t.\tA\t4\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig'))
self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t5\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))
self.assertTrue(v10.update_indel(pymummer.snp.Snp('4\t.\tT\t6\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig')))

mummer_variants = [[v0], [v1], [v2], [v3], [v4], [v5], [v6], [v7], [v8], [v9], [v10]]

Expand Down Expand Up @@ -306,8 +306,8 @@ def test_get_variants_presence_absence(self):
os.unlink(metadata_tsv)

nucmer_snp_file = os.path.join(data_dir, 'assembly_variants_test_get_variants_presence_absence.snps')
v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig1'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig1'))
v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig1'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tX\tX\t42\t42\tX\tX\tpresence_absence\tcontig1'))

ref_nucmer_coords = {
'contig1': [pyfastaq.intervals.Interval(0, 30)],
Expand Down Expand Up @@ -354,8 +354,8 @@ def test_get_variants_variants_only(self):
os.unlink(metadata_tsv)

nucmer_snp_file = os.path.join(data_dir, 'assembly_variants_test_get_variants_variants_only.snps')
v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tvariants_only\tcontig1'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tx\tx\t42\t42\tx\tx\tvariants_only\tcontig1'))
v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tX\tX\t42\t42\tX\tX\tvariants_only\tcontig1'))
v3 = pymummer.variant.Variant(pymummer.snp.Snp('15\tG\tC\t15\tX\tX\t42\t42\tX\tX\tvariants_only\tcontig1'))

ctg_nucmer_coords = {
'contig1': [pyfastaq.intervals.Interval(0, 41)],
Expand Down

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