Merge pull request #124 from martinghunt/report_ref_base_assembled_bug

Bug fix reporting ref_base_assembled for a partial gene assembly
sanger-pathogens · Aug 16, 2016 · 2473895 · 2473895
2 parents b6d5ae7 + 9dc4405
commit 2473895
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Showing 7 changed files with 890 additions and 1 deletion.
diff --git a/ariba/report.py b/ariba/report.py
@@ -137,8 +137,9 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum
     lines = []
     contig_length = len(cluster.assembly.sequences[contig_name])
     assert contig_length != 0
+
     if contig_name in ref_cov_per_contig:
-        if contig_name == cluster.assembly_compare.scaff_name_matching_ref:
+        if contig_name == cluster.assembly_compare.scaff_name_matching_ref and cluster.assembly_compare.gene_matching_ref_type == 'GENE_FOUND':
             ref_cov = len(cluster.ref_sequence)
         else:
             ref_cov = ref_cov_per_contig[contig_name]

diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py
@@ -443,3 +443,20 @@ def test_full_run_cluster_test_full_run_smtls_snp_varonly_nonc(self):
         ]
         self.assertEqual(expected, c.report_lines)
         shutil.rmtree(tmpdir)
+
+
+    def test_full_run_partial_assembly(self):
+        '''Test complete run where only part of the ref gene is present in the reads'''
+        fasta_in = os.path.join(data_dir, 'cluster_test_full_run_partial_asmbly.fa')
+        tsv_in = os.path.join(data_dir, 'cluster_test_full_run_partial_asmbly.tsv')
+        refdata = reference_data.ReferenceData([fasta_in], [tsv_in])
+        tmpdir = 'tmp.cluster_test_full_run_partial_assembly'
+        shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_partial_asmbly'), tmpdir)
+        c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=278, total_reads_bases=15020)
+        c.run()
+
+        expected = [
+            'presence_absence1\t1\t0\t19\t278\tcluster_name\t96\t77\t100.0\tcluster_name.scaffold.1\t949\t20.5\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tGeneric description of presence_absence1'
+        ]
+        self.assertEqual(expected, c.report_lines)
+        shutil.rmtree(tmpdir)
diff --git a/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa b/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa
@@ -0,0 +1,3 @@
+>presence_absence1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
diff --git a/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv b/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv
@@ -0,0 +1 @@
+presence_absence1	1	0	.	.	Generic description of presence_absence1
diff --git a/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq b/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq
diff --git a/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq b/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq
diff --git a/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa b/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa
@@ -0,0 +1,3 @@
+>presence_absence1
+ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT
+ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		presence_absence1 1 0 . . Generic description of presence_absence1