mirror of
https://github.com/biopython/biopython.git
synced 2025-10-21 06:23:48 +08:00
57056bbfc4
Reverted unwanted changes (mostly arrays in tests, but also some whitespace in doctests). Remaining changes are standardising spacing between module docstring and imports, and lower-case \x<hex> in strings.
93 lines
3.2 KiB
Python
93 lines
3.2 KiB
Python
# 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 of the transcription and translation methods of Seq objects."""
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import unittest
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from Bio import Seq
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class TestTranscriptionTranslation(unittest.TestCase):
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def test_transcription(self):
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s = "ATA"
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dna = Seq.Seq(s)
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rna = dna.transcribe()
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self.assertEqual(rna, "AUA")
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s = "GAAAATTCATTTTCTTTGGACTTTCTCTGAAATCCGAGTCCTAGGAAAGATGCGTGAGATTCTTCATATT"
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dna = Seq.Seq(s)
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rna = dna.transcribe()
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self.assertEqual(
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rna,
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"GAAAAUUCAUUUUCUUUGGACUUUCUCUGAAAUCCGAGUCCUAGGAAAGAUGCGUGAGAUUCUUCAUAUU",
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)
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s = "GAAAAUUCAUUUUCUUUGGACUUUCUCUGAAAUCCGAGUCCUAGGAAAGAUGCGUGAGAUUCUUCAUAUU"
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rna = Seq.Seq(s)
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dna = rna.back_transcribe()
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self.assertEqual(
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dna,
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"GAAAATTCATTTTCTTTGGACTTTCTCTGAAATCCGAGTCCTAGGAAAGATGCGTGAGATTCTTCATATT",
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)
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def test_translation(self):
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s = ""
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dna = Seq.Seq(s)
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protein = dna.translate(to_stop=True)
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self.assertEqual(protein, "")
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s = "TAA"
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dna = Seq.Seq(s)
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protein = dna.translate(to_stop=True)
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self.assertEqual(protein, "")
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s = "GAAAATTCATTTTCTTTGGACTTTCTCTGAAATCCGAGTCCTAGGAAAGATGCGTGAGATTCTTCA"
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dna = Seq.Seq(s)
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protein = dna.translate(to_stop=True)
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self.assertEqual(protein, "ENSFSLDFL")
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s = "GAA"
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dna = Seq.Seq(s)
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protein = dna.translate(15, to_stop=True)
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self.assertEqual(protein, "E")
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s = "ATA"
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dna = Seq.Seq(s)
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protein = dna.translate("Vertebrate Mitochondrial", to_stop=True)
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self.assertEqual(protein, "M")
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s = "GAAAATTCATTTTCTTTGGACTTTCTCTGAAATCCGAGTCCTAGGAAAGATGCGTGAGATTCTTCATAT"
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dna = Seq.Seq(s)
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protein = dna.translate("SGC8", to_stop=True)
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self.assertEqual(protein, "ENSFSLDFLWNPSPSNDAWDSSY")
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def test_dna_rna_translation(self):
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s = "TCAAAAAGGTGCATCTAGATG"
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dna = Seq.Seq(s)
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protein = dna.translate(to_stop=True)
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self.assertEqual(protein, "SKRCI")
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gapped_protein = dna.translate()
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self.assertEqual(gapped_protein, "SKRCI*M")
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# The table used here has "AGG" as a stop codon:
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p2 = dna.translate(table=2, to_stop=True)
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self.assertEqual(p2, "SK")
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p2 = dna.translate(table=2)
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self.assertEqual(p2, "SK*CI*M")
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p2 = dna.translate(table=2, stop_symbol="+")
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self.assertEqual(p2, "SK+CI+M")
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r = s.replace("T", "U")
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rna = Seq.Seq(r)
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protein = rna.translate(to_stop=True)
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self.assertEqual(protein, "SKRCI")
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gapped_protein = rna.translate()
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self.assertEqual(gapped_protein, "SKRCI*M")
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def test_ambiguous(self):
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s = "RATGATTARAATYTA"
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dna = Seq.Seq(s)
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protein = dna.translate("Vertebrate Mitochondrial")
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self.assertEqual(protein, "BD*NL")
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stop_protein = dna.translate("SGC1", to_stop=True)
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self.assertEqual(stop_protein, "BD")
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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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