Add a FastqName class to create and parse standardized fastq names.

[htsworkflow.git] / htsworkflow / submission / test / test_fastqname.py

diff --git a/htsworkflow/submission/test/test_fastqname.py b/htsworkflow/submission/test/test_fastqname.py
new file mode 100644 (file)
index 0000000..d51ad0e
--- /dev/null
+++ b/htsworkflow/submission/test/test_fastqname.py
@@ -0,0 +1,109 @@
+from unittest2 import TestCase
+from htsworkflow.submission.fastqname import FastqName
+
+class TestFastqName(TestCase):
+    def test_init_empty(self):
+        fq = FastqName()
+        self.assertEqual(fq.is_valid, False)
+
+    def test_init_single_filename(self):
+        fq = FastqName(filename="12345_AABBCCDDXX_c100_l1.fastq")
+        self.assertEqual(fq.lib_id, "12345")
+        self.assertEqual(fq['lib_id'], "12345")
+        self.assertEqual(fq.flowcell, "AABBCCDDXX")
+        self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+        self.assertEqual(fq.cycle, "100")
+        self.assertEqual(fq['cycle'], "100")
+        self.assertEqual(fq.lane, "1")
+        self.assertEqual(fq['lane'], "1")
+        self.assertEqual(fq.is_paired, False)
+
+    def test_init_single_filename(self):
+        fq = FastqName(filename="12345_AABBCCDDXX_c100_l1_r2.fastq")
+        self.assertEqual(fq.lib_id, "12345")
+        self.assertEqual(fq['lib_id'], "12345")
+        self.assertEqual(fq.flowcell, "AABBCCDDXX")
+        self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+        self.assertEqual(fq.cycle, "100")
+        self.assertEqual(fq['cycle'], "100")
+        self.assertEqual(fq.lane, "1")
+        self.assertEqual(fq['lane'], "1")
+        self.assertEqual(fq.read, "2")
+        self.assertEqual(fq['read'], "2")
+        self.assertEqual(fq.is_paired, True)
+
+    def test_init_bad_filename(self):
+        attribs = {'filename': 'asdf.bam'}
+        self.assertRaises(ValueError, FastqName, **attribs)
+
+    def test_init_single_attributes(self):
+        fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+                       cycle = "100", lane="1")
+        self.assertEqual(fq.is_valid, True)
+        self.assertEqual(fq.lib_id, "12345")
+        self.assertEqual(fq['lib_id'], "12345")
+        self.assertEqual(fq.flowcell, "AABBCCDDXX")
+        self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+        self.assertEqual(fq.cycle, "100")
+        self.assertEqual(fq['cycle'], "100")
+        self.assertEqual(fq.lane, "1")
+        self.assertEqual(fq['lane'], "1")
+        self.assertEqual(fq.is_paired, False)
+        self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1.fastq")
+
+    def test_init_single_attributes_set_single(self):
+        fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+                       cycle = "100", lane="1", is_paired=False)
+        self.assertEqual(fq.is_valid, True)
+        self.assertEqual(fq.is_paired, False)
+
+    def test_init_single_attributes_set_paired(self):
+        fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+                       cycle = "100", lane="1", is_paired=True)
+        self.assertEqual(fq.is_valid, False)
+        self.assertEqual(fq.is_paired, True)
+
+    def test_init_paired_attributes(self):
+        fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+                       cycle = "100", lane="1", read="2")
+        self.assertEqual(fq.is_valid, True)
+        self.assertEqual(fq.lib_id, "12345")
+        self.assertEqual(fq['lib_id'], "12345")
+        self.assertEqual(fq.flowcell, "AABBCCDDXX")
+        self.assertEqual(fq['flowcell'], "AABBCCDDXX")
+        self.assertEqual(fq.cycle, "100")
+        self.assertEqual(fq['cycle'], "100")
+        self.assertEqual(fq.lane, "1")
+        self.assertEqual(fq['lane'], "1")
+        self.assertEqual(fq.read, "2")
+        self.assertEqual(fq['read'], "2")
+        self.assertEqual(fq.is_paired, True)
+        self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1_r2.fastq")
+
+    def test_init_paired_attributes_set_single(self):
+        fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+                       cycle = "100", lane="1", read="2", is_paired=False)
+        self.assertEqual(fq.is_valid, True)
+        self.assertEqual(fq.is_paired, False)
+
+    def test_init_paired_attributes_set_paired(self):
+        fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
+                       cycle = "100", lane="1", read="2", is_paired=True)
+        self.assertEqual(fq.is_valid, True)
+        self.assertEqual(fq.is_paired, True)
+
+    def test_init_insufficient_attributes(self):
+        attribs = dict(lib_id="12345", flowcell="AABBCCDDXX")
+        fq = FastqName(**attribs)
+        self.assertEqual(fq.is_valid, False)
+
+
+def suite():
+    from unittest2 import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName))
+    return suite
+
+if __name__ == "__main__":
+    from unittest2 import main
+    main(defaultTest='suite')