# Copyright 2001 by Brad Chapman. All rights reserved. # Revisions copyright 2008-2009 by Michiel de Hoon. All rights reserved. # Revisions copyright 2010-2011 by Peter Cock. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Primer-based programs in the Emboss suite.""" # standard library import os import unittest # local stuff from Bio.Emboss import PrimerSearch, Primer3 class Primer3ParseTest(unittest.TestCase): def setUp(self): self.test_files = [ os.path.join("Emboss", "bac_find.primer3"), os.path.join("Emboss", "cds_forward.primer3"), os.path.join("Emboss", "cds_reverse.primer3"), os.path.join("Emboss", "short.primer3"), os.path.join("Emboss", "internal_oligo.primer3"), os.path.join("Emboss", "no_oligo.primer3"), ] def test_simple_parse(self): """Make sure that we can use all single target primer3 files.""" for file in self.test_files: # First using read... with open(file) as handle: Primer3.read(handle) # Now using parse... with open(file) as handle: self.assertEqual(1, len(list(Primer3.parse(handle)))) def test_indepth_regular_parse(self): """Make sure we get the data from normal primer3 files okay.""" regular_file = self.test_files[0] with open(regular_file) as handle: primer_info = Primer3.read(handle) self.assertEqual(len(primer_info.primers), 5) self.assertEqual(primer_info.comments, "# PRIMER3 RESULTS FOR AC074298\n") self.assertEqual(primer_info.primers[1].forward_seq, "CCGGTTTCTCTGGTTGAAAA") self.assertEqual(primer_info.primers[2].reverse_seq, "TCACATTCCCAAATGTAGATCG") self.assertEqual(primer_info.primers[0].size, 218) self.assertEqual(len(primer_info.primers[0]), 218) self.assertEqual(primer_info.primers[3].forward_start, 112) self.assertEqual(primer_info.primers[3].forward_length, 20) self.assertEqual(primer_info.primers[3].forward_tm, 59.57) self.assertEqual(primer_info.primers[3].forward_gc, 45.00) self.assertEqual(primer_info.primers[4].reverse_start, 304) self.assertEqual(primer_info.primers[4].reverse_length, 22) self.assertEqual(primer_info.primers[4].reverse_tm, 59.61) self.assertEqual(primer_info.primers[4].reverse_gc, 40.91) def test_in_depth_single_parse(self): """Make sure we get info right from a single primer find.""" file = self.test_files[1] with open(file) as handle: primer_info = Primer3.read(handle) self.assertEqual(len(primer_info.primers), 5) self.assertEqual(primer_info.comments, "# PRIMER3 RESULTS FOR 26964-28647#\n") self.assertEqual(primer_info.primers[1].reverse_seq, "") self.assertEqual(primer_info.primers[1].internal_seq, "") self.assertEqual(primer_info.primers[3].forward_seq, "TGTGATTGCTTGAGCTGGAC") self.assertEqual(primer_info.primers[3].internal_seq, "") self.assertEqual(primer_info.primers[3].forward_start, 253) def test_internal_oligo_single_parse(self): """Make sure we can parse an internal oligo file correctly.""" # these files are generated when designing hybridization probes. file = self.test_files[4] with open(file) as handle: primer_info = Primer3.read(handle) self.assertEqual(len(primer_info.primers), 5) self.assertEqual(primer_info.comments, "# EPRIMER3 RESULTS FOR YNL138W-A\n") self.assertEqual(primer_info.primers[0].internal_length, 22) self.assertEqual(primer_info.primers[1].internal_seq, "TTGCGCTTTAGTTTGAATTGAA") self.assertEqual(primer_info.primers[2].internal_tm, 58.62) self.assertEqual(primer_info.primers[3].internal_start, 16) self.assertEqual(primer_info.primers[4].internal_gc, 35.00) def test_multi_record_fwd(self): """Test parsing multiple primer sets (NirK forward).""" with open(os.path.join("Emboss", "NirK.primer3")) as handle: targets = list(Primer3.parse(handle)) self.assertEqual(len(targets), 16) for target in targets: self.assertEqual(len(target.primers), 5) self.assertEqual(targets[0].primers[0].forward_seq, "GCAAACTGAAAAGCGGACTC") self.assertEqual(targets[0].primers[1].forward_seq, "GGGACGTACTTTCGCACAAT") self.assertEqual(targets[0].primers[2].forward_seq, "GTCTTATGCGTGGTGGAGGT") self.assertEqual(targets[0].primers[3].forward_seq, "GTACATCAACATCCGCAACG") self.assertEqual(targets[0].primers[4].forward_seq, "CGTACATCAACATCCGCAAC") self.assertEqual(targets[1].primers[0].forward_seq, "GGAAGTGCTTCTCGTTTTCG") self.assertEqual(targets[1].primers[1].forward_seq, "TACAGAGCGTCACGGATGAG") self.assertEqual(targets[1].primers[2].forward_seq, "TTGTCATCGTGCTCTTCGTC") self.assertEqual(targets[1].primers[3].forward_seq, "GACTCCAACCTCAGCTTTCG") self.assertEqual(targets[1].primers[4].forward_seq, "GGCACGAAGAAGGACAGAAG") self.assertEqual(targets[15].primers[0].forward_seq, "TGCTTGAAAATGACGCACTC") self.assertEqual(targets[15].primers[1].forward_seq, "CTCGCTGGCTAGGTCATAGG") self.assertEqual(targets[15].primers[2].forward_seq, "TATCGCACCAAACACGGTAA") self.assertEqual(targets[15].primers[3].forward_seq, "CGATTACCCTCACCGTCACT") self.assertEqual(targets[15].primers[4].forward_seq, "TATCGCAACCACTGAGCAAG") def test_multi_record_full(self): """Test parsing multiple primer sets (NirK full).""" with open(os.path.join("Emboss", "NirK_full.primer3")) as handle: targets = list(Primer3.parse(handle)) self.assertEqual(len(targets), 16) for target in targets: self.assertEqual(len(target.primers), 5) self.assertEqual(targets[15].primers[0].forward_seq, "ACTCACTTCGGCTGAATGCT") self.assertEqual(targets[15].primers[1].forward_seq, "GGCGATTAGCGCTGTCTATC") self.assertEqual(targets[15].primers[2].forward_seq, "ACTCACTTCGGCTGAATGCT") self.assertEqual(targets[15].primers[3].forward_seq, "TAGGCGTATAGACCGGGTTG") self.assertEqual(targets[15].primers[4].forward_seq, "AGCAAGCTGACCACTGGTTT") self.assertEqual(targets[15].primers[0].reverse_seq, "CATTTAATCCGGATGCCAAC") self.assertEqual(targets[15].primers[1].reverse_seq, "TGGCCTTTCTCTCCTCTTCA") self.assertEqual(targets[15].primers[2].reverse_seq, "ATTTAATCCGGATGCCAACA") self.assertEqual(targets[15].primers[3].reverse_seq, "CACACATTATTGGCGGTCAC") self.assertEqual(targets[15].primers[4].reverse_seq, "TCTGAAACCACCAAGGAAGC") self.assertEqual(targets[15].primers[0].internal_seq, "CCCACCAATATTTGGCTAGC") self.assertEqual(targets[15].primers[1].internal_seq, "AATCTTCTGTGCACCTTGCC") self.assertEqual(targets[15].primers[2].internal_seq, "CCCACCAATATTTGGCTAGC") self.assertEqual(targets[15].primers[3].internal_seq, "TGAGCCTGTGTTCCACACAT") self.assertEqual(targets[15].primers[4].internal_seq, "CTATGCCCTTCTGCCACAAT") class PrimersearchParseTest(unittest.TestCase): def setUp(self): self.test_files = [os.path.join("Emboss", "bac_find.psearch")] def test_simple_parse(self): """Make sure that we can parse all primersearch files.""" for file in self.test_files: with open(file) as handle: PrimerSearch.read(handle) def test_in_depth_normal_parse(self): """Make sure the output from a simple primersearch file is correct.""" file = self.test_files[0] with open(file) as handle: amp_info = PrimerSearch.read(handle) self.assertEqual(len(amp_info.amplifiers), 1) self.assertIn("Test", amp_info.amplifiers) self.assertEqual(len(amp_info.amplifiers["Test"]), 1) self.assertEqual(amp_info.amplifiers["Test"][0].length, 218) self.assertEqual( amp_info.amplifiers["Test"][0].hit_info, "AC074298 AC074298 \n" "\tTelomere associated sequence for Arabidopsis thaliana " "TEL1N from chromosome I, complete sequence.\n" "\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 " "with 0 mismatches\n" "\tTCACATTCCCAAATGTAGATCG hits reverse strand at " "[114] with 0 mismatches", ) class PrimerSearchInputTest(unittest.TestCase): """Test creating input files for primersearch.""" def setUp(self): pass def test_primer_representation(self): """Make sure we can output primer information correctly.""" p_info = PrimerSearch.InputRecord() p_info.add_primer_set("Test", "GATC", "CATG") p_info.add_primer_set("Test2", "AATA", "TTAT") output = str(p_info) self.assertEqual(output, "Test GATC CATG\nTest2 AATA TTAT\n") if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)