[med-svn] [Git][med-team/filtlong][master] Add temporary patch to fix tests
Pranav Ballaney
gitlab at salsa.debian.org
Thu May 14 17:56:08 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / filtlong
Commits:
c4cb00b2 by Pranav Ballaney at 2020-05-14T22:23:59+05:30
Add temporary patch to fix tests
- - - - -
2 changed files:
- + debian/patches/ignore_locales_in_test_output.patch
- + debian/patches/series
Changes:
=====================================
debian/patches/ignore_locales_in_test_output.patch
=====================================
@@ -0,0 +1,296 @@
+--- a/test/test_sort.py
++++ b/test/test_sort.py
+@@ -90,7 +90,7 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 100,000 bp' in console_out)
++ self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
+ self.assertTrue('not enough reads to reach target' in console_out)
+
+ def test_sort_high_threshold_1_assembly_ref(self):
+@@ -98,7 +98,7 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 100,000 bp' in console_out)
++ self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
+ self.assertTrue('not enough reads to reach target' in console_out)
+
+ def test_sort_high_threshold_1_read_ref(self):
+@@ -106,7 +106,7 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 100,000 bp' in console_out)
++ self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
+ self.assertTrue('not enough reads to reach target' in console_out)
+
+ def test_sort_high_threshold_1_assembly_ref_fasta(self):
+@@ -114,7 +114,7 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 100,000 bp' in console_out)
++ self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
+ self.assertTrue('not enough reads to reach target' in console_out)
+
+ def test_sort_high_threshold_1_read_ref_fasta(self):
+@@ -122,7 +122,7 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 100000 bp' in console_out)
++ self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
+ self.assertTrue('not enough reads to reach target' in console_out)
+
+ def test_sort_high_threshold_2(self):
+@@ -133,40 +133,40 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 10,001 bp' in console_out)
+- self.assertTrue('keeping 15,000 bp' in console_out)
++ self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
+
+ def test_sort_high_threshold_2_assembly_ref(self):
+ console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 10001 INPUT > OUTPUT.fastq')
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 10,001 bp' in console_out)
+- self.assertTrue('keeping 15,000 bp' in console_out)
++ self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
+
+ def test_sort_high_threshold_2_read_ref(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 10001 INPUT > OUTPUT.fastq')
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 10,001 bp' in console_out)
+- self.assertTrue('keeping 15,000 bp' in console_out)
++ self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
+
+ def test_sort_high_threshold_2_assembly_ref_fasta(self):
+ console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 10001 FASTA > OUTPUT.fastq')
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 10,001 bp' in console_out)
+- self.assertTrue('keeping 15,000 bp' in console_out)
++ self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
+
+ def test_sort_high_threshold_2_read_ref_fasta(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 10001 FASTA > OUTPUT.fastq')
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 10,001 bp' in console_out)
+- self.assertTrue('keeping 15,000 bp' in console_out)
++ self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_1(self):
+ """
+@@ -177,8 +177,8 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 10,000 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_1_assembly_ref(self):
+ """
+@@ -188,32 +188,32 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
+- self.assertTrue('target: 10,000 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_1_read_ref(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 10000 INPUT > OUTPUT.fastq')
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
+- self.assertTrue('target: 10,000 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_1_assembly_ref_fasta(self):
+ console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 10000 FASTA > OUTPUT.fastq')
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
+- self.assertTrue('target: 10,000 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_1_read_ref_fasta(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 10000 FASTA > OUTPUT.fastq')
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
+- self.assertTrue('target: 10,000 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_2(self):
+ """
+@@ -223,8 +223,8 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_2', 'test_sort_3'])
+- self.assertTrue('target: 5,001 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_2_assembly_ref(self):
+ """
+@@ -234,32 +234,32 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
+- self.assertTrue('target: 5,001 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_2_read_ref(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 5001 INPUT > OUTPUT.fastq')
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
+- self.assertTrue('target: 5,001 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_2_assembly_ref_fasta(self):
+ console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 5001 FASTA > OUTPUT.fastq')
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
+- self.assertTrue('target: 5,001 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_medium_threshold_2_read_ref_fasta(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 5001 FASTA > OUTPUT.fastq')
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
+- self.assertTrue('target: 5,001 bp' in console_out)
+- self.assertTrue('keeping 10,000 bp' in console_out)
++ self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_1(self):
+ """
+@@ -269,8 +269,8 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_2'])
+- self.assertTrue('target: 5,000 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_1_assembly_ref(self):
+ """
+@@ -280,32 +280,32 @@ class TestSort(unittest.TestCase):
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1'])
+- self.assertTrue('target: 5,000 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_1_read_ref(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 5000 INPUT > OUTPUT.fastq')
+ output_reads = load_fastq(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1'])
+- self.assertTrue('target: 5,000 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_1_assembly_ref_fasta(self):
+ console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 5000 FASTA > OUTPUT.fastq')
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1'])
+- self.assertTrue('target: 5,000 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_1_read_ref_fasta(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 5000 FASTA > OUTPUT.fastq')
+ output_reads = load_fasta(self.output_file)
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1'])
+- self.assertTrue('target: 5,000 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_2(self):
+ """
+@@ -316,7 +316,7 @@ class TestSort(unittest.TestCase):
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_2'])
+ self.assertTrue('target: 1 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_2_assembly_ref(self):
+ """
+@@ -327,7 +327,7 @@ class TestSort(unittest.TestCase):
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1'])
+ self.assertTrue('target: 1 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_2_read_ref(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 1 INPUT > OUTPUT.fastq')
+@@ -335,7 +335,7 @@ class TestSort(unittest.TestCase):
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1'])
+ self.assertTrue('target: 1 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_2_assembly_ref_fasta(self):
+ console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 1 FASTA > OUTPUT.fastq')
+@@ -343,7 +343,7 @@ class TestSort(unittest.TestCase):
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1'])
+ self.assertTrue('target: 1 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
+
+ def test_sort_low_threshold_2_read_ref_fasta(self):
+ console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 1 FASTA > OUTPUT.fastq')
+@@ -351,4 +351,4 @@ class TestSort(unittest.TestCase):
+ read_names = [x[0].decode() for x in output_reads]
+ self.assertEqual(read_names, ['test_sort_1'])
+ self.assertTrue('target: 1 bp' in console_out)
+- self.assertTrue('keeping 5,000 bp' in console_out)
++ self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+ignore_locales_in_test_output.patch
View it on GitLab: https://salsa.debian.org/med-team/filtlong/-/commit/c4cb00b2a995785b5189e2464e15cd35681cc086
--
View it on GitLab: https://salsa.debian.org/med-team/filtlong/-/commit/c4cb00b2a995785b5189e2464e15cd35681cc086
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