From ad9a6ce412bae55797e3cc07dac1bcc29d1bcc23 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 27 Nov 2018 11:48:40 -0500 Subject: [PATCH] add unit tests for reading feature id from tbl file --- test/input/TestFeatureReader/GU481072.1.tbl | 14 +++++++++++++ test/input/TestFeatureReader/GU481073.1.tbl | 14 +++++++++++++ test/input/TestFeatureReader/KM821772.1.tbl | 14 +++++++++++++ test/input/TestFeatureReader/KM821773.1.tbl | 14 +++++++++++++ test/input/TestFeatureReader/NC_026438.1.tbl | 9 ++++++++ test/input/TestFeatureReader/test1-S.tbl | 14 +++++++++++++ test/input/TestFeatureReader/test2-L.tbl | 14 +++++++++++++ test/unit/test_ncbi.py | 22 ++++++++++++++++++++ 8 files changed, 115 insertions(+) create mode 100644 test/input/TestFeatureReader/GU481072.1.tbl create mode 100644 test/input/TestFeatureReader/GU481073.1.tbl create mode 100644 test/input/TestFeatureReader/KM821772.1.tbl create mode 100644 test/input/TestFeatureReader/KM821773.1.tbl create mode 100644 test/input/TestFeatureReader/NC_026438.1.tbl create mode 100644 test/input/TestFeatureReader/test1-S.tbl create mode 100644 test/input/TestFeatureReader/test2-L.tbl diff --git a/test/input/TestFeatureReader/GU481072.1.tbl b/test/input/TestFeatureReader/GU481072.1.tbl new file mode 100644 index 000000000..a88e7b6e5 --- /dev/null +++ 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 new file mode 100644 index 000000000..6dced5cfa --- /dev/null +++ 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 new file mode 100644 index 000000000..6df807d26 --- /dev/null +++ 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 new file mode 100644 index 000000000..2c105a405 --- /dev/null +++ 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 new file mode 100644 index 000000000..c25b577f9 --- /dev/null +++ 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 new file mode 100644 index 000000000..61ed90ce0 --- /dev/null +++ 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 new file mode 100644 index 000000000..c0c5f9052 --- /dev/null +++ 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 index 44f650e0e..3fbd42a34 100644 --- 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()