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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
198 lines
9.1 KiB
Python
198 lines
9.1 KiB
Python
# Copyright 2001 by Brad Chapman. All rights reserved.
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# Revisions copyright 2008-2009 by Michiel de Hoon. All rights reserved.
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# Revisions copyright 2010-2011 by Peter Cock. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Tests for Primer-based programs in the Emboss suite."""
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# standard library
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import os
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import unittest
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from Bio.Emboss import Primer3
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# local stuff
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from Bio.Emboss import PrimerSearch
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class Primer3ParseTest(unittest.TestCase):
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def setUp(self):
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self.test_files = [
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os.path.join("Emboss", "bac_find.primer3"),
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os.path.join("Emboss", "cds_forward.primer3"),
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os.path.join("Emboss", "cds_reverse.primer3"),
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os.path.join("Emboss", "short.primer3"),
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os.path.join("Emboss", "internal_oligo.primer3"),
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os.path.join("Emboss", "no_oligo.primer3"),
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]
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def test_simple_parse(self):
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"""Make sure that we can use all single target primer3 files."""
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for file in self.test_files:
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# First using read...
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with open(file) as handle:
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Primer3.read(handle)
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# Now using parse...
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with open(file) as handle:
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self.assertEqual(1, len(list(Primer3.parse(handle))))
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def test_indepth_regular_parse(self):
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"""Make sure we get the data from normal primer3 files okay."""
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regular_file = self.test_files[0]
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with open(regular_file) as handle:
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primer_info = Primer3.read(handle)
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self.assertEqual(len(primer_info.primers), 5)
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self.assertEqual(primer_info.comments, "# PRIMER3 RESULTS FOR AC074298\n")
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self.assertEqual(primer_info.primers[1].forward_seq, "CCGGTTTCTCTGGTTGAAAA")
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self.assertEqual(primer_info.primers[2].reverse_seq, "TCACATTCCCAAATGTAGATCG")
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self.assertEqual(primer_info.primers[0].size, 218)
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self.assertEqual(len(primer_info.primers[0]), 218)
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self.assertEqual(primer_info.primers[3].forward_start, 112)
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self.assertEqual(primer_info.primers[3].forward_length, 20)
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self.assertEqual(primer_info.primers[3].forward_tm, 59.57)
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self.assertEqual(primer_info.primers[3].forward_gc, 45.00)
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self.assertEqual(primer_info.primers[4].reverse_start, 304)
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self.assertEqual(primer_info.primers[4].reverse_length, 22)
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self.assertEqual(primer_info.primers[4].reverse_tm, 59.61)
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self.assertEqual(primer_info.primers[4].reverse_gc, 40.91)
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def test_in_depth_single_parse(self):
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"""Make sure we get info right from a single primer find."""
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file = self.test_files[1]
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with open(file) as handle:
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primer_info = Primer3.read(handle)
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self.assertEqual(len(primer_info.primers), 5)
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self.assertEqual(primer_info.comments, "# PRIMER3 RESULTS FOR 26964-28647#\n")
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self.assertEqual(primer_info.primers[1].reverse_seq, "")
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self.assertEqual(primer_info.primers[1].internal_seq, "")
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self.assertEqual(primer_info.primers[3].forward_seq, "TGTGATTGCTTGAGCTGGAC")
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self.assertEqual(primer_info.primers[3].internal_seq, "")
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self.assertEqual(primer_info.primers[3].forward_start, 253)
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def test_internal_oligo_single_parse(self):
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"""Make sure we can parse an internal oligo file correctly."""
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# these files are generated when designing hybridization probes.
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file = self.test_files[4]
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with open(file) as handle:
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primer_info = Primer3.read(handle)
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self.assertEqual(len(primer_info.primers), 5)
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self.assertEqual(primer_info.comments, "# EPRIMER3 RESULTS FOR YNL138W-A\n")
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self.assertEqual(primer_info.primers[0].internal_length, 22)
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self.assertEqual(primer_info.primers[1].internal_seq, "TTGCGCTTTAGTTTGAATTGAA")
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self.assertEqual(primer_info.primers[2].internal_tm, 58.62)
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self.assertEqual(primer_info.primers[3].internal_start, 16)
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self.assertEqual(primer_info.primers[4].internal_gc, 35.00)
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def test_multi_record_fwd(self):
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"""Test parsing multiple primer sets (NirK forward)."""
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with open(os.path.join("Emboss", "NirK.primer3")) as handle:
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targets = list(Primer3.parse(handle))
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self.assertEqual(len(targets), 16)
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for target in targets:
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self.assertEqual(len(target.primers), 5)
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self.assertEqual(targets[0].primers[0].forward_seq, "GCAAACTGAAAAGCGGACTC")
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self.assertEqual(targets[0].primers[1].forward_seq, "GGGACGTACTTTCGCACAAT")
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self.assertEqual(targets[0].primers[2].forward_seq, "GTCTTATGCGTGGTGGAGGT")
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self.assertEqual(targets[0].primers[3].forward_seq, "GTACATCAACATCCGCAACG")
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self.assertEqual(targets[0].primers[4].forward_seq, "CGTACATCAACATCCGCAAC")
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self.assertEqual(targets[1].primers[0].forward_seq, "GGAAGTGCTTCTCGTTTTCG")
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self.assertEqual(targets[1].primers[1].forward_seq, "TACAGAGCGTCACGGATGAG")
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self.assertEqual(targets[1].primers[2].forward_seq, "TTGTCATCGTGCTCTTCGTC")
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self.assertEqual(targets[1].primers[3].forward_seq, "GACTCCAACCTCAGCTTTCG")
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self.assertEqual(targets[1].primers[4].forward_seq, "GGCACGAAGAAGGACAGAAG")
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self.assertEqual(targets[15].primers[0].forward_seq, "TGCTTGAAAATGACGCACTC")
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self.assertEqual(targets[15].primers[1].forward_seq, "CTCGCTGGCTAGGTCATAGG")
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self.assertEqual(targets[15].primers[2].forward_seq, "TATCGCACCAAACACGGTAA")
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self.assertEqual(targets[15].primers[3].forward_seq, "CGATTACCCTCACCGTCACT")
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self.assertEqual(targets[15].primers[4].forward_seq, "TATCGCAACCACTGAGCAAG")
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def test_multi_record_full(self):
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"""Test parsing multiple primer sets (NirK full)."""
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with open(os.path.join("Emboss", "NirK_full.primer3")) as handle:
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targets = list(Primer3.parse(handle))
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self.assertEqual(len(targets), 16)
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for target in targets:
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self.assertEqual(len(target.primers), 5)
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self.assertEqual(targets[15].primers[0].forward_seq, "ACTCACTTCGGCTGAATGCT")
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self.assertEqual(targets[15].primers[1].forward_seq, "GGCGATTAGCGCTGTCTATC")
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self.assertEqual(targets[15].primers[2].forward_seq, "ACTCACTTCGGCTGAATGCT")
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self.assertEqual(targets[15].primers[3].forward_seq, "TAGGCGTATAGACCGGGTTG")
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self.assertEqual(targets[15].primers[4].forward_seq, "AGCAAGCTGACCACTGGTTT")
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self.assertEqual(targets[15].primers[0].reverse_seq, "CATTTAATCCGGATGCCAAC")
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self.assertEqual(targets[15].primers[1].reverse_seq, "TGGCCTTTCTCTCCTCTTCA")
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self.assertEqual(targets[15].primers[2].reverse_seq, "ATTTAATCCGGATGCCAACA")
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self.assertEqual(targets[15].primers[3].reverse_seq, "CACACATTATTGGCGGTCAC")
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self.assertEqual(targets[15].primers[4].reverse_seq, "TCTGAAACCACCAAGGAAGC")
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self.assertEqual(targets[15].primers[0].internal_seq, "CCCACCAATATTTGGCTAGC")
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self.assertEqual(targets[15].primers[1].internal_seq, "AATCTTCTGTGCACCTTGCC")
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self.assertEqual(targets[15].primers[2].internal_seq, "CCCACCAATATTTGGCTAGC")
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self.assertEqual(targets[15].primers[3].internal_seq, "TGAGCCTGTGTTCCACACAT")
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self.assertEqual(targets[15].primers[4].internal_seq, "CTATGCCCTTCTGCCACAAT")
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class PrimersearchParseTest(unittest.TestCase):
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def setUp(self):
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self.test_files = [os.path.join("Emboss", "bac_find.psearch")]
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def test_simple_parse(self):
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"""Make sure that we can parse all primersearch files."""
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for file in self.test_files:
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with open(file) as handle:
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PrimerSearch.read(handle)
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def test_in_depth_normal_parse(self):
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"""Make sure the output from a simple primersearch file is correct."""
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file = self.test_files[0]
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with open(file) as handle:
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amp_info = PrimerSearch.read(handle)
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self.assertEqual(len(amp_info.amplifiers), 1)
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self.assertIn("Test", amp_info.amplifiers)
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self.assertEqual(len(amp_info.amplifiers["Test"]), 1)
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self.assertEqual(amp_info.amplifiers["Test"][0].length, 218)
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self.assertEqual(
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amp_info.amplifiers["Test"][0].hit_info,
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"AC074298 AC074298 \n"
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"\tTelomere associated sequence for Arabidopsis thaliana "
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"TEL1N from chromosome I, complete sequence.\n"
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"\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 "
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"with 0 mismatches\n"
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"\tTCACATTCCCAAATGTAGATCG hits reverse strand at "
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"[114] with 0 mismatches",
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)
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class PrimerSearchInputTest(unittest.TestCase):
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"""Test creating input files for primersearch."""
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def setUp(self):
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pass
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def test_primer_representation(self):
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"""Make sure we can output primer information correctly."""
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p_info = PrimerSearch.InputRecord()
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p_info.add_primer_set("Test", "GATC", "CATG")
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p_info.add_primer_set("Test2", "AATA", "TTAT")
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output = str(p_info)
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self.assertEqual(output, "Test GATC CATG\nTest2 AATA TTAT\n")
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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