diff tests/test_ribocount.py @ 12:61c47a1d6a7a

Add a test to check if a valid FASTA file is used (ribocount)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/test_ribocount.py	Wed Aug 19 11:11:37 2015 +0100
@@ -0,0 +1,25 @@
+import os
+import logging
+import unittest
+
+from riboplot import ribocore, riboplot, ribocount
+
+# use testing configuration
+CONFIG = ribocount.CONFIG = riboplot.config.TestingConfig()
+logging.disable(logging.CRITICAL)
+
+RIBO_FILE = os.path.join(CONFIG.DATA_DIR, '5hRPFsorted.bam')
+RNA_FILE = os.path.join(CONFIG.DATA_DIR, '5hmRNAsorted.bam')
+TRANSCRIPT_NAME = 'gi|148357119|ref|NM_001098396.1|'
+TRANSCRIPTOME_FASTA = os.path.join(CONFIG.DATA_DIR, 'zebrafish.fna')
+TRANSCRIPTOME_FASTA_MINUS1 = os.path.join(CONFIG.DATA_DIR, 'zebrafish_minus1.fna')
+UNRELATED_FASTA = os.path.join(CONFIG.DATA_DIR, 'unrelated.fna')
+
+
+class RiboCountTestCase(unittest.TestCase):
+
+    def test_unrelated_fasta_file(self):
+        """If an unrelated fasta file is used, raise an error"""
+        parser = ribocount.create_parser()
+        args = parser.parse_args(['-b', RIBO_FILE, '-f', UNRELATED_FASTA])
+        self.assertRaises(ribocore.ArgumentError, ribocount.main, args)