# Revisions copyright 2009 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 Phd module.""" import unittest from Bio import SeqIO from Bio.Sequencing import Phd class PhdTestOne(unittest.TestCase): def setUp(self): self.handle = open("Phd/phd1") def tearDown(self): self.handle.close() def test_check_SeqIO(self): """Test phd1 using parser via SeqIO.""" records = SeqIO.parse(self.handle, "phd") # Contig 1 record = next(records) self.assertEqual(record.id, "34_222_(80-A03-19).b.ab1") self.assertEqual(record.name, "34_222_(80-A03-19).b.ab1") self.assertEqual(record.description, "34_222_(80-A03-19).b.ab1") self.assertTrue(record.seq.startswith("ctccgtcggaacatcatcggatcctatcaca")) self.assertTrue(record.seq.endswith("ctctcctctccctccctccgactccaaagcgtg")) self.assertEqual( record.letter_annotations["phred_quality"][:10], [9, 9, 10, 19, 22, 37, 28, 28, 24, 22], ) self.assertEqual( record[:10].format("fasta"), ">34_222_(80-A03-19).b.ab1\nctccgtcgga\n" ) self.assertEqual( record[:10].format("qual"), ">34_222_(80-A03-19).b.ab1\n9 9 10 19 22 37 28 28 24 22\n", ) self.assertEqual( record[:10].format("fastq"), "@34_222_(80-A03-19).b.ab1\nctccgtcgga\n+\n**+47F==97\n", ) self.assertEqual( record[:10].format("fastq-illumina"), "@34_222_(80-A03-19).b.ab1\nctccgtcgga\n+\nIIJSVe\\\\XV\n", ) # Contig 2 record = next(records) self.assertEqual(record.id, "425_103_(81-A03-19).g.ab1") self.assertEqual(record.name, "425_103_(81-A03-19).g.ab1") self.assertEqual( record.letter_annotations["phred_quality"][:10], [14, 17, 22, 10, 10, 10, 15, 8, 8, 9], ) # Contig 3 record = next(records) self.assertEqual(record.id, "425_7_(71-A03-19).b.ab1") self.assertEqual(record.name, "425_7_(71-A03-19).b.ab1") self.assertEqual( record.letter_annotations["phred_quality"][:10], [10, 10, 10, 10, 8, 8, 6, 6, 6, 6], ) # Make sure that no further records are found self.assertRaises(StopIteration, next, records) def test_check_record_parser(self): """Test phd1 file in detail.""" records = Phd.parse(self.handle) # Record 1 record = next(records) self.assertEqual(record.file_name, "34_222_(80-A03-19).b.ab1") self.assertEqual(record.comments["abi_thumbprint"], 0) self.assertEqual(record.comments["call_method"], "phred") self.assertEqual(record.comments["chem"], "term") self.assertEqual(record.comments["chromat_file"], "34_222_(80-A03-19).b.ab1") self.assertEqual(record.comments["dye"], "big") self.assertEqual(record.comments["phred_version"], "0.020425.c") self.assertEqual(record.comments["quality_levels"], 99) self.assertEqual(record.comments["time"], "Fri Feb 13 09:16:11 2004") self.assertEqual(record.comments["trace_array_max_index"], 10867) self.assertEqual(record.comments["trace_array_min_index"], 0) self.assertAlmostEqual(record.comments["trace_peak_area_ratio"], 0.1467) self.assertEqual(record.comments["trim"][0], 3) self.assertEqual(record.comments["trim"][1], 391) self.assertAlmostEqual(record.comments["trim"][2], 0.05) center = len(record.sites) // 2 self.assertEqual(record.sites[0], ("c", "9", "6")) self.assertEqual(record.sites[1], ("t", "9", "18")) self.assertEqual(record.sites[2], ("c", "10", "26")) self.assertEqual(record.sites[3], ("c", "19", "38")) self.assertEqual(record.sites[4], ("g", "22", "49")) self.assertEqual(record.sites[5], ("t", "37", "65")) self.assertEqual(record.sites[6], ("c", "28", "76")) self.assertEqual(record.sites[7], ("g", "28", "87")) self.assertEqual(record.sites[8], ("g", "24", "100")) self.assertEqual(record.sites[9], ("a", "22", "108")) self.assertEqual(record.sites[center - 5], ("c", "11", "5259")) self.assertEqual(record.sites[center - 4], ("c", "11", "5273")) self.assertEqual(record.sites[center - 3], ("t", "9", "5286")) self.assertEqual(record.sites[center - 2], ("g", "10", "5300")) self.assertEqual(record.sites[center - 1], ("a", "10", "5316")) self.assertEqual(record.sites[center], ("t", "8", "5323")) self.assertEqual(record.sites[center + 1], ("c", "8", "5343")) self.assertEqual(record.sites[center + 2], ("g", "8", "5352")) self.assertEqual(record.sites[center + 3], ("c", "8", "5366")) self.assertEqual(record.sites[center + 4], ("c", "8", "5378")) self.assertEqual(record.sites[-10], ("c", "8", "10756")) self.assertEqual(record.sites[-9], ("c", "8", "10764")) self.assertEqual(record.sites[-8], ("a", "8", "10769")) self.assertEqual(record.sites[-7], ("a", "8", "10788")) self.assertEqual(record.sites[-6], ("a", "8", "10803")) self.assertEqual(record.sites[-5], ("g", "10", "10816")) self.assertEqual(record.sites[-4], ("c", "11", "10826")) self.assertEqual(record.sites[-3], ("g", "11", "10840")) self.assertEqual(record.sites[-2], ("t", "11", "10855")) self.assertEqual(record.sites[-1], ("g", "11", "10864")) self.assertEqual(str(record.seq)[:10], "ctccgtcgga") self.assertEqual(str(record.seq)[-10:], "ccaaagcgtg") self.assertEqual(str(record.seq_trimmed)[:10], "cgtcggaaca") self.assertEqual(str(record.seq_trimmed)[-10:], "tatttcggag") # Record 2 record = next(records) center = len(record.sites) // 2 self.assertEqual(record.file_name, "425_103_(81-A03-19).g.ab1") self.assertEqual(record.comments["abi_thumbprint"], 0) self.assertEqual(record.comments["call_method"], "phred") self.assertEqual(record.comments["chem"], "term") self.assertEqual(record.comments["chromat_file"], "425_103_(81-A03-19).g.ab1") self.assertEqual(record.comments["dye"], "big") self.assertEqual(record.comments["phred_version"], "0.020425.c") self.assertEqual(record.comments["quality_levels"], 99) self.assertEqual(record.comments["time"], "Tue Feb 17 10:31:15 2004") self.assertEqual(record.comments["trace_array_max_index"], 10606) self.assertEqual(record.comments["trace_array_min_index"], 0) self.assertAlmostEqual(record.comments["trace_peak_area_ratio"], 0.0226) self.assertEqual(record.comments["trim"][0], 10) self.assertEqual(record.comments["trim"][1], 432) self.assertAlmostEqual(record.comments["trim"][2], 0.05) self.assertEqual(record.sites[0], ("c", "14", "3")) self.assertEqual(record.sites[1], ("g", "17", "11")) self.assertEqual(record.sites[2], ("g", "22", "23")) self.assertEqual(record.sites[3], ("g", "10", "35")) self.assertEqual(record.sites[4], ("a", "10", "53")) self.assertEqual(record.sites[5], ("t", "10", "68")) self.assertEqual(record.sites[6], ("c", "15", "75")) self.assertEqual(record.sites[7], ("c", "8", "85")) self.assertEqual(record.sites[8], ("c", "8", "94")) self.assertEqual(record.sites[9], ("a", "9", "115")) self.assertEqual(record.sites[center - 5], ("c", "33", "5140")) self.assertEqual(record.sites[center - 4], ("c", "28", "5156")) self.assertEqual(record.sites[center - 3], ("g", "25", "5167")) self.assertEqual(record.sites[center - 2], ("c", "28", "5178")) self.assertEqual(record.sites[center - 1], ("c", "18", "5193")) self.assertEqual(record.sites[center], ("a", "16", "5204")) self.assertEqual(record.sites[center + 1], ("a", "15", "5213")) self.assertEqual(record.sites[center + 2], ("a", "10", "5230")) self.assertEqual(record.sites[center + 3], ("a", "10", "5242")) self.assertEqual(record.sites[center + 4], ("t", "8", "5249")) self.assertEqual(record.sites[-10], ("c", "8", "10489")) self.assertEqual(record.sites[-9], ("c", "8", "10503")) self.assertEqual(record.sites[-8], ("c", "8", "10514")) self.assertEqual(record.sites[-7], ("a", "8", "10516")) self.assertEqual(record.sites[-6], ("g", "8", "10530")) self.assertEqual(record.sites[-5], ("c", "8", "10550")) self.assertEqual(record.sites[-4], ("c", "10", "10566")) self.assertEqual(record.sites[-3], ("a", "8", "10574")) self.assertEqual(record.sites[-2], ("a", "7", "10584")) self.assertEqual(record.sites[-1], ("g", "7", "10599")) self.assertEqual(str(record.seq)[:10], "cgggatccca") self.assertEqual(str(record.seq)[-10:], "cccagccaag") self.assertEqual(str(record.seq_trimmed)[:10], "cctgatccga") self.assertEqual(str(record.seq_trimmed)[-10:], "ggggccgcca") # Record 3 record = next(records) center = len(record.sites) // 2 self.assertEqual(record.file_name, "425_7_(71-A03-19).b.ab1") self.assertEqual(record.comments["abi_thumbprint"], 0) self.assertEqual(record.comments["call_method"], "phred") self.assertEqual(record.comments["chem"], "term") self.assertEqual(record.comments["chromat_file"], "425_7_(71-A03-19).b.ab1") self.assertEqual(record.comments["dye"], "big") self.assertEqual(record.comments["phred_version"], "0.020425.c") self.assertEqual(record.comments["quality_levels"], 99) self.assertEqual(record.comments["time"], "Thu Jan 29 11:46:14 2004") self.assertEqual(record.comments["trace_array_max_index"], 9513) self.assertEqual(record.comments["trace_array_min_index"], 0) self.assertAlmostEqual(record.comments["trace_peak_area_ratio"], 100.0) self.assertEqual(record.comments["trim"][0], -1) self.assertEqual(record.comments["trim"][1], -1) self.assertEqual(record.comments["trim"][2], 0.05) self.assertEqual(record.sites[0], ("a", "10", "7")) self.assertEqual(record.sites[1], ("c", "10", "13")) self.assertEqual(record.sites[2], ("a", "10", "21")) self.assertEqual(record.sites[3], ("t", "10", "28")) self.assertEqual(record.sites[4], ("a", "8", "33")) self.assertEqual(record.sites[5], ("a", "8", "40")) self.assertEqual(record.sites[6], ("a", "6", "50")) self.assertEqual(record.sites[7], ("t", "6", "53")) self.assertEqual(record.sites[8], ("c", "6", "66")) self.assertEqual(record.sites[9], ("a", "6", "68")) self.assertEqual(record.sites[center - 5], ("a", "6", "4728")) self.assertEqual(record.sites[center - 4], ("t", "10", "4737")) self.assertEqual(record.sites[center - 3], ("a", "10", "4746")) self.assertEqual(record.sites[center - 2], ("a", "8", "4756")) self.assertEqual(record.sites[center - 1], ("t", "8", "4759")) self.assertEqual(record.sites[center], ("t", "8", "4768")) self.assertEqual(record.sites[center + 1], ("a", "8", "4775")) self.assertEqual(record.sites[center + 2], ("g", "10", "4783")) self.assertEqual(record.sites[center + 3], ("t", "8", "4788")) self.assertEqual(record.sites[center + 4], ("g", "8", "4794")) self.assertEqual(record.sites[-10], ("a", "8", "9445")) self.assertEqual(record.sites[-9], ("t", "6", "9453")) self.assertEqual(record.sites[-8], ("c", "6", "9462")) self.assertEqual(record.sites[-7], ("t", "6", "9465")) self.assertEqual(record.sites[-6], ("g", "6", "9478")) self.assertEqual(record.sites[-5], ("c", "6", "9483")) self.assertEqual(record.sites[-4], ("t", "6", "9485")) self.assertEqual(record.sites[-3], ("t", "8", "9495")) self.assertEqual(record.sites[-2], ("t", "3", "9504")) self.assertEqual(record.sites[-1], ("n", "0", "9511")) self.assertEqual(str(record.seq)[:10], "acataaatca") self.assertEqual(str(record.seq)[-10:], "atctgctttn") # Make sure that no further records are found self.assertRaises(StopIteration, next, records) class PhdTestTwo(unittest.TestCase): def setUp(self): self.handle = open("Phd/phd2") def tearDown(self): self.handle.close() def test_check_SeqIO(self): """Test phd2 using parser via SeqIO.""" records = SeqIO.parse(self.handle, "phd") # Contig 1 record = next(records) self.assertEqual(record.id, "ML4924R") self.assertEqual(record.name, "ML4924R") self.assertEqual(record.description, "ML4924R") self.assertTrue(record.seq.startswith("actttggtcgcctgcaggtaccggtccgnga")) self.assertTrue(record.seq.endswith("agaagctcgttctcaacatctccgttggtgaga")) self.assertEqual( record.letter_annotations["phred_quality"][:10], [6, 6, 6, 8, 8, 12, 18, 16, 14, 11], ) self.assertEqual(record[:10].format("fasta"), ">ML4924R\nactttggtcg\n") self.assertEqual( record[:10].format("qual"), ">ML4924R\n6 6 6 8 8 12 18 16 14 11\n" ) self.assertEqual( record[:10].format("fastq"), "@ML4924R\nactttggtcg\n+\n'''))-31/,\n" ) self.assertEqual( record[:10].format("fastq-illumina"), "@ML4924R\nactttggtcg\n+\nFFFHHLRPNK\n", ) # Make sure that no further records are found self.assertRaises(StopIteration, next, records) class PhdTest454(unittest.TestCase): def setUp(self): self.handle = open("Phd/phd_454") def tearDown(self): self.handle.close() def test_check_SeqIO(self): """Test phd_454 using parser via SeqIO.""" records = SeqIO.parse(self.handle, "phd") # Contig 1 record = next(records) self.assertEqual(record.id, "EBE03TV04IHLTF.77-243") self.assertEqual(record.name, "EBE03TV04IHLTF.77-243") self.assertEqual(record.description, "EBE03TV04IHLTF.77-243 1") self.assertEqual(str(record.seq), "ggggatgaaagggatctcggtggtaggtga") self.assertEqual( record.letter_annotations["phred_quality"][:10], [37, 37, 37, 37, 37, 37, 37, 37, 37, 37], ) self.assertEqual( record.format("fasta"), ">EBE03TV04IHLTF.77-243 1\nggggatgaaagggatctcggtggtaggtga\n", ) self.assertEqual( record.format("qual"), ">EBE03TV04IHLTF.77-243 1\n" "37 37 37 37 37 37 37 37 37 37 " "37 37 37 26 26 26 30 33 33 33\n" "33 33 36 36 33 33 33 36 26 22\n", ) self.assertEqual( record.format("fastq"), "@EBE03TV04IHLTF.77-243 1\n" "ggggatgaaagggatctcggtggtaggtga\n" "+\n" "FFFFFFFFFFFFF;;;?BBBBBEEBBBE;7\n", ) self.assertEqual( record[:10].format("fastq-illumina"), "@EBE03TV04IHLTF.77-243 1\nggggatgaaa\n+\neeeeeeeeee\n", ) # Make sure that no further records are found self.assertRaises(StopIteration, next, records) class PhdTestSolexa(unittest.TestCase): def setUp(self): self.handle = open("Phd/phd_solexa") def tearDown(self): self.handle.close() def test_check_SeqIO(self): """Test phd2 using parser via SeqIO.""" records = SeqIO.parse(self.handle, "phd") # Contig 1 record = next(records) self.assertEqual(record.id, "HWI-EAS94_4_1_1_537_446") self.assertEqual(record.name, "HWI-EAS94_4_1_1_537_446") self.assertEqual(record.description, "HWI-EAS94_4_1_1_537_446 1") self.assertEqual(str(record.seq), "gccaatcaggtttctctgcaagcccctttagcagctgagc") self.assertEqual( record.letter_annotations["phred_quality"], [ 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 28, 23, 30, 30, 30, 30, 30, 30, 28, 22, 8, 22, 7, 15, 15, 15, 10, 10, 11, 15, ], ) self.assertEqual( record.format("fasta"), ">HWI-EAS94_4_1_1_537_446 1\ngccaatcaggtttctctgcaagcccctttagcagctgagc\n", ) self.assertEqual( record.format("qual"), ">HWI-EAS94_4_1_1_537_446 1\n" "30 30 30 30 30 30 30 30 30 30 " "30 30 30 30 30 30 30 30 30 30\n" "28 23 30 30 30 30 30 30 28 22 " "8 22 7 15 15 15 10 10 11 15\n", ) self.assertEqual( record.format("fastq"), "@HWI-EAS94_4_1_1_537_446 1\n" "gccaatcaggtttctctgcaagcccctttagcagctgagc\n" "+\n" "????????????????????=8??????=7)7(000++,0\n", ) self.assertEqual( record.format("fastq-illumina"), "@HWI-EAS94_4_1_1_537_446 1\n" "gccaatcaggtttctctgcaagcccctttagcagctgagc\n" "+\n" "^^^^^^^^^^^^^^^^^^^^\\W^^^^^^\\VHVGOOOJJKO\n", ) # Contig 2 record = next(records) self.assertEqual(record.id, "HWI-EAS94_4_1_1_602_99") self.assertEqual(record.name, "HWI-EAS94_4_1_1_602_99") self.assertEqual(record.description, "HWI-EAS94_4_1_1_602_99 1") self.assertEqual(str(record.seq), "gccatggcacatatatgaaggtcagaggacaacttgctgt") self.assertEqual( record.letter_annotations["phred_quality"], [ 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 30, 28, 22, 22, 22, 14, 15, 15, 5, 10, 15, 10, 5, ], ) self.assertEqual( record.format("fasta"), ">HWI-EAS94_4_1_1_602_99 1\ngccatggcacatatatgaaggtcagaggacaacttgctgt\n", ) self.assertEqual( record.format("qual"), ">HWI-EAS94_4_1_1_602_99 1\n" "30 30 30 30 30 30 30 30 30 30 " "30 30 30 30 30 30 30 30 30 30\n" "30 30 30 30 30 30 16 30 28 22 " "22 22 14 15 15 5 10 15 10 5\n", ) self.assertEqual( record.format("fastq"), "@HWI-EAS94_4_1_1_602_99 1\n" "gccatggcacatatatgaaggtcagaggacaacttgctgt\n" "+\n" "??????????????????????????1?=777/00&+0+&\n", ) self.assertEqual( record.format("fastq-illumina"), "@HWI-EAS94_4_1_1_602_99 1\n" "gccatggcacatatatgaaggtcagaggacaacttgctgt\n" "+\n" "^^^^^^^^^^^^^^^^^^^^^^^^^^P^\\VVVNOOEJOJE\n", ) # Make sure that no further records are found self.assertRaises(StopIteration, next, records) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)