If a quality score started with an @ sign it was treated as a header

[htsworkflow.git] / test / test_srf2fastq.py

diff --git a/test/test_srf2fastq.py b/test/test_srf2fastq.py
new file mode 100644 (file)
index 0000000..f29cc70
--- /dev/null
+++ b/test/test_srf2fastq.py
@@ -0,0 +1,119 @@
+import os
+from StringIO import StringIO
+import sys
+import unittest
+
+_module_path, _module_name = os.path.split(__file__)
+sys.path.append(os.path.join(_module_path, '..', 'scripts'))
+
+import srf2named_fastq
+
+class testSrf2Fastq(unittest.TestCase):
+    def test_split_good(self):
+        source = StringIO("""@header
+AGCTTTTT
++
+IIIIB+++
+""")
+        target1 = StringIO()
+        target2 = StringIO()
+
+        srf2named_fastq.convert_single_to_two_fastq(source, target1, target2)
+
+        target1.seek(0)
+        lines1 = target1.readlines()
+        self.failUnlessEqual(len(lines1),4)
+        self.failUnlessEqual(lines1[0].rstrip(), '@header/1')
+        self.failUnlessEqual(lines1[1].rstrip(), 'AGCT')
+        self.failUnlessEqual(lines1[2].rstrip(), '+')
+        self.failUnlessEqual(lines1[3].rstrip(), 'IIII')
+
+        target2.seek(0)
+        lines2 = target2.readlines()
+        self.failUnlessEqual(len(lines2),4)
+        self.failUnlessEqual(lines2[0].rstrip(), '@header/2')
+        self.failUnlessEqual(lines2[1].rstrip(), 'TTTT')
+        self.failUnlessEqual(lines2[2].rstrip(), '+')
+        self.failUnlessEqual(lines2[3].rstrip(), 'B+++')
+
+    def test_split_at_with_header(self):
+        source = StringIO("""@header1
+AGCTTTTT
++
+@IIIB+++
+@header2
+AGCTTTTT
++
+IIIIB+++
+""")
+        target1 = StringIO()
+        target2 = StringIO()
+
+        srf2named_fastq.convert_single_to_two_fastq(source, target1, target2, header="foo_")
+
+        target1.seek(0)
+        lines1 = target1.readlines()
+        self.failUnlessEqual(len(lines1),8)
+        self.failUnlessEqual(lines1[0].rstrip(), '@foo_header1/1')
+        self.failUnlessEqual(lines1[1].rstrip(), 'AGCT')
+        self.failUnlessEqual(lines1[2].rstrip(), '+')
+        self.failUnlessEqual(lines1[3].rstrip(), '@III')
+
+        target2.seek(0)
+        lines2 = target2.readlines()
+        self.failUnlessEqual(len(lines2),8)
+        self.failUnlessEqual(lines2[0].rstrip(), '@foo_header1/2')
+        self.failUnlessEqual(lines2[1].rstrip(), 'TTTT')
+        self.failUnlessEqual(lines2[2].rstrip(), '+')
+        self.failUnlessEqual(lines2[3].rstrip(), 'B+++')
+
+    def test_single_at(self):
+        source = StringIO("""@header1
+AGCTTTTT
++
+@IIIB+++
+@header2
+AGCTTTTT
++
+IIIIB+++
+""")
+        target1 = StringIO()
+
+        srf2named_fastq.convert_single_to_fastq(source, target1)
+
+        target1.seek(0)
+        lines1 = target1.readlines()
+        self.failUnlessEqual(len(lines1),8)
+        self.failUnlessEqual(lines1[0].rstrip(), '@header1')
+        self.failUnlessEqual(lines1[1].rstrip(), 'AGCTTTTT')
+        self.failUnlessEqual(lines1[2].rstrip(), '+')
+        self.failUnlessEqual(lines1[3].rstrip(), '@IIIB+++')
+
+    def test_single_at_with_header(self):
+        source = StringIO("""@header1
+AGCTTTTT
++
+@IIIB+++
+@header2
+AGCTTTTT
++
+IIIIB+++
+""")
+        target1 = StringIO()
+
+        srf2named_fastq.convert_single_to_fastq(source, target1, header="foo_")
+
+        target1.seek(0)
+        lines1 = target1.readlines()
+        self.failUnlessEqual(len(lines1),8)
+        self.failUnlessEqual(lines1[0].rstrip(), '@foo_header1')
+        self.failUnlessEqual(lines1[1].rstrip(), 'AGCTTTTT')
+        self.failUnlessEqual(lines1[2].rstrip(), '+')
+        self.failUnlessEqual(lines1[3].rstrip(), '@IIIB+++')
+
+
+def suite():
+    return unittest.makeSuite(testSrf2Fastq,'test')
+
+if __name__ == "__main__":
+    unittest.main(defaultTest="suite")