| 4 | 4 |
pymummer now, we need to catch up even though upstream does not.
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| 5 | 5 |
Author: Sascha Steinbiss <satta@debian.org>
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| 6 | 6 |
Last-Update: 2020-06-30
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| 7 | |
--- a/ariba/tests/assembly_variants_test.py
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| 8 | |
+++ b/ariba/tests/assembly_variants_test.py
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| 9 | |
@@ -52,23 +52,23 @@
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|
7 |
Index: ariba/ariba/tests/assembly_variants_test.py
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|
8 |
===================================================================
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|
9 |
--- ariba.orig/ariba/tests/assembly_variants_test.py
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|
10 |
+++ ariba/ariba/tests/assembly_variants_test.py
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|
11 |
@@ -52,23 +52,23 @@ class TestAssemblyVariants(unittest.Test
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| 10 | 12 |
def test_get_variant_effect(self):
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| 11 | 13 |
'''test _get_variant_effect'''
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| 12 | 14 |
ref_seq = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA')
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|
| 42 | 44 |
v11.ref_base = 'CGCGAA'
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| 43 | 45 |
v11.ref_end = 8
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| 44 | 46 |
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| 45 | |
@@ -93,9 +93,9 @@
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47 |
@@ -93,9 +93,9 @@ class TestAssemblyVariants(unittest.Test
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| 46 | 48 |
def test_filter_mummer_variants(self):
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| 47 | 49 |
'''test filter_mummer_variants'''
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| 48 | 50 |
ref_seq = pyfastaq.sequences.Fasta('gene', 'GATCGCGAAGCGATGACCCATGAAGCGACCGAACGCTGA')
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| 55 | 57 |
mummer_variants = {'contig': [[v1, v2], v3]}
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| 56 | 58 |
assembly_variants.AssemblyVariants._filter_mummer_variants(mummer_variants, ref_seq)
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| 57 | 59 |
expected = {'contig': [[v1, v2]]}
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| 58 | |
@@ -110,13 +110,13 @@
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|
60 |
@@ -110,13 +110,13 @@ class TestAssemblyVariants(unittest.Test
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| 59 | 61 |
ref_sequence_name = 'non_coding'
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| 60 | 62 |
refdata_var_dict = refdata.metadata[ref_sequence_name]
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| 61 | 63 |
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| 72 | 74 |
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| 73 | 75 |
meta0 = sequence_metadata.SequenceMetadata('non_coding\t0\t0\tC3A\tid1\tref has variant type A')
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| 74 | 76 |
meta2 = sequence_metadata.SequenceMetadata('non_coding\t0\t0\tT5A\tid1\tref has wild type T')
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| 75 | |
@@ -153,33 +153,33 @@
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|
77 |
@@ -153,33 +153,33 @@ class TestAssemblyVariants(unittest.Test
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| 76 | 78 |
ref_sequence = refdata.sequence(ref_sequence_name)
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| 77 | 79 |
refdata_var_dict = refdata.metadata[ref_sequence_name]
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| 78 | 80 |
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| 133 | 135 |
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| 134 | 136 |
mummer_variants = [[v0], [v1], [v2], [v3], [v4], [v5], [v6], [v7], [v8], [v9], [v10]]
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| 135 | 137 |
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| 136 | |
@@ -306,8 +306,8 @@
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|
138 |
@@ -306,8 +306,8 @@ class TestAssemblyVariants(unittest.Test
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| 137 | 139 |
os.unlink(metadata_tsv)
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| 138 | 140 |
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| 139 | 141 |
nucmer_snp_file = os.path.join(data_dir, 'assembly_variants_test_get_variants_presence_absence.snps')
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|
| 144 | 146 |
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| 145 | 147 |
ref_nucmer_coords = {
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| 146 | 148 |
'contig1': [pyfastaq.intervals.Interval(0, 30)],
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| 147 | |
@@ -354,8 +354,8 @@
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|
149 |
@@ -354,8 +354,8 @@ class TestAssemblyVariants(unittest.Test
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| 148 | 150 |
os.unlink(metadata_tsv)
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| 149 | 151 |
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| 150 | 152 |
nucmer_snp_file = os.path.join(data_dir, 'assembly_variants_test_get_variants_variants_only.snps')
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|
| 155 | 157 |
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| 156 | 158 |
ctg_nucmer_coords = {
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| 157 | 159 |
'contig1': [pyfastaq.intervals.Interval(0, 41)],
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| 158 | |
--- a/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps
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| 159 | |
+++ b/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps
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|
160 |
Index: ariba/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps
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|
161 |
===================================================================
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|
162 |
--- ariba.orig/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps
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|
163 |
+++ ariba/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps
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| 160 | 164 |
@@ -1,3 +1,3 @@
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| 161 | 165 |
-9 A T 9 x x 42 42 x x variants_only contig1
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| 162 | 166 |
-14 C A 14 x x 42 42 x x variants_only contig1
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|
| 164 | 168 |
+9 A T 9 x x 42 42 x 1 variants_only contig1
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| 165 | 169 |
+14 C A 14 x x 42 42 x 1 variants_only contig1
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| 166 | 170 |
+15 G C 15 x x 42 42 x 1 variants_only contig1
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| 167 | |
--- a/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps
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| 168 | |
+++ b/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps
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|
171 |
Index: ariba/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps
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|
172 |
===================================================================
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|
173 |
--- ariba.orig/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps
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|
174 |
+++ ariba/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps
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| 169 | 175 |
@@ -1,3 +1,3 @@
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| 170 | 176 |
-9 A T 9 x x 42 42 x x presence_absence contig1
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| 171 | 177 |
-14 C A 14 x x 42 42 x x presence_absence contig1
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