Merge a32be51 into 5dbd9fc

broadinstitute · Nov 27, 2018 · 255e014 · 255e014
2 parents 5dbd9fc + a32be51
commit 255e014
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Showing 9 changed files with 116 additions and 1 deletion.
diff --git a/test/input/TestFeatureReader/GU481072.1.tbl b/test/input/TestFeatureReader/GU481072.1.tbl
@@ -0,0 +1,14 @@
+>Feature gb|GU481072.1|
+52	1524	gene
+			gene_desc	GPC
+52	1524	CDS
+			product	glycoprotein precursor
+			transl_table	1
+			protein_id	gb|ADU56618.1|
+3294	1585	gene
+			gene_desc	NP
+3294	1585	CDS
+			product	nucleoprotein
+			transl_table	1
+			protein_id	gb|ADU56619.1|
+
diff --git a/test/input/TestFeatureReader/GU481073.1.tbl b/test/input/TestFeatureReader/GU481073.1.tbl
@@ -0,0 +1,14 @@
+>Feature gb|GU481073.1|
+46	345	gene
+			gene_desc	Z
+46	345	CDS
+			product	Z protein
+			transl_table	1
+			protein_id	gb|ADU56620.1|
+7116	448	gene
+			gene_desc	L
+7116	448	CDS
+			product	polymerase
+			transl_table	1
+			protein_id	gb|ADU56621.1|
+
diff --git a/test/input/TestFeatureReader/KM821772.1.tbl b/test/input/TestFeatureReader/KM821772.1.tbl
@@ -0,0 +1,14 @@
+>Feature gb|KM821772.1|
+57	356	gene
+			gene	Z
+57	356	CDS
+			product	Z protein
+			transl_table	1
+			protein_id	gb|AIT17124.1|
+7118	456	gene
+			gene	L
+7118	456	CDS
+			product	polymerase
+			transl_table	1
+			protein_id	gb|AIT17125.1|
+
diff --git a/test/input/TestFeatureReader/KM821773.1.tbl b/test/input/TestFeatureReader/KM821773.1.tbl
@@ -0,0 +1,14 @@
+>Feature gb|KM821773.1|
+48	1523	gene
+			gene	GPC
+48	1523	CDS
+			product	glycoprotein precursor
+			transl_table	1
+			protein_id	gb|AIT17126.1|
+3294	1585	gene
+			gene	NP
+3294	1585	CDS
+			product	nucleoprotein
+			transl_table	1
+			protein_id	gb|AIT17127.1|
+
diff --git a/test/input/TestFeatureReader/NC_026438.1.tbl b/test/input/TestFeatureReader/NC_026438.1.tbl
@@ -0,0 +1,9 @@
+>Feature ref|NC_026438.1|
+1	2280	gene
+			gene	PB2
+			locus_tag	UJ99_s1gp1
+			db_xref	GeneID:23308131
+1	2280	CDS
+			product	polymerase PB2
+			protein_id	ref|YP_009118631.1|
+
diff --git a/test/input/TestFeatureReader/test1-S.tbl b/test/input/TestFeatureReader/test1-S.tbl
@@ -0,0 +1,14 @@
+>Feature gb|KM821998.1|
+59	1531	gene
+			gene	GPC
+59	1531	CDS
+			product	glycoprotein precursor
+			transl_table	1
+			protein_id	gb|AIT17576.1|
+3308	1599	gene
+			gene	NP
+3308	1599	CDS
+			product	nucleoprotein
+			transl_table	1
+			protein_id	gb|AIT17577.1|
+
diff --git a/test/input/TestFeatureReader/test2-L.tbl b/test/input/TestFeatureReader/test2-L.tbl
@@ -0,0 +1,14 @@
+>Feature gb|KM821997.1|
+76	375	gene
+			gene	Z
+76	375	CDS
+			product	Z protein
+			transl_table	1
+			protein_id	gb|AIT17574.1|
+7132	470	gene
+			gene	L
+7132	470	CDS
+			product	polymerase
+			transl_table	1
+			protein_id	gb|AIT17575.1|
+
diff --git a/test/unit/test_ncbi.py b/test/unit/test_ncbi.py
@@ -11,6 +11,7 @@
 # module-specific
 import ncbi
 import util.file
+import util.genbank
 from test import assert_equal_bam_reads, TestCaseWithTmp, assert_equal_contents, assert_md5_equal_to_line_in_file
 
 
@@ -21,6 +22,27 @@ def test_help_parser_for_each_command(self):
             parser = parser_fun(argparse.ArgumentParser())
             helpstring = parser.format_help()
 
+class TestFeatureReader(TestCaseWithTmp):
+    def setUp(self):
+        super(TestFeatureReader, self).setUp()
+        self.input_dir = util.file.get_test_input_path(self)
+
+    def test_read_seq_id_simple(self):
+        accessions = ('GU481072.1', 'GU481073.1',
+            'KM821772.1', 'KM821773.1')
+        for acc in accessions:
+            self.assertEqual(acc, util.genbank.get_feature_table_id(os.path.join(self.input_dir, acc+'.tbl')))
+
+    def test_read_seq_id_different_fnames(self):
+        self.assertEqual('KM821998.1', util.genbank.get_feature_table_id(os.path.join(self.input_dir,
+            'test1-S.tbl')))
+        self.assertEqual('KM821997.1', util.genbank.get_feature_table_id(os.path.join(self.input_dir,
+            'test2-L.tbl')))
+
+    def test_read_seq_id_refseq(self):
+        self.assertEqual('NC_026438.1', util.genbank.get_feature_table_id(os.path.join(self.input_dir,
+            'NC_026438.1.tbl')))
+
 class TestFeatureTransfer(TestCaseWithTmp):
     def setUp(self):
         super(TestFeatureTransfer, self).setUp()

diff --git a/util/genbank.py b/util/genbank.py
@@ -36,7 +36,7 @@ def get_feature_table_id(featureTableFile):
                 if not (
                     (seqid.startswith('gb|') or seqid.startswith('ref|'))):
                     raise Exception("reference annotation ID does not appear to refer to a GenBank or RefSeq accession: %s" % seqid)
-                m = re.search(r"(?P<db>(?:gb|ref))\|(?:(?P<accession>[a-zA-Z0-9\.]+))+.*", seqid)
+                m = re.search(r"(?P<db>(?:gb|ref|dbj))\|(?:(?P<accession>[a-zA-Z0-9\._]+))+.*", seqid)
                 if m:
                    seqid = m.group("accession")
                 else: