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# Copyright 2008 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.
from __future__ import print_function
from Bio.Data import IUPACData
from Bio.Data.CodonTable import ambiguous_generic_by_id, ambiguous_generic_by_name
from Bio.Data.CodonTable import ambiguous_rna_by_id, ambiguous_dna_by_id
from Bio.Data.CodonTable import unambiguous_rna_by_id
from Bio.Data.CodonTable import list_ambiguous_codons, TranslationError
# Check the extension of stop codons to include well defined ambiguous ones
assert list_ambiguous_codons(['TGA', 'TAA'], IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TRA']
assert list_ambiguous_codons(['TAG', 'TGA'], IUPACData.ambiguous_dna_values) == ['TAG', 'TGA']
assert list_ambiguous_codons(['TAG', 'TAA'], IUPACData.ambiguous_dna_values) == ['TAG', 'TAA', 'TAR']
assert list_ambiguous_codons(['UAG', 'UAA'], IUPACData.ambiguous_rna_values) == ['UAG', 'UAA', 'UAR']
assert list_ambiguous_codons(['TGA', 'TAA', 'TAG'], IUPACData.ambiguous_dna_values) == ['TGA', 'TAA', 'TAG', 'TAR', 'TRA']
# Basic sanity test,
for n in ambiguous_generic_by_id:
assert ambiguous_rna_by_id[n].forward_table["GUU"] == "V"
assert ambiguous_rna_by_id[n].forward_table["GUN"] == "V"
if n != 23:
assert ambiguous_rna_by_id[n].forward_table["UUN"] == "X" # F or L
assert ambiguous_dna_by_id[n].forward_table["GTT"] == "V"
if n != 23:
assert ambiguous_dna_by_id[n].forward_table["TTN"] == "X" # F or L
assert ambiguous_dna_by_id[n].forward_table["GTN"] == "V"
if n != 23:
assert ambiguous_generic_by_id[n].forward_table.get("TTN") == "X"
assert ambiguous_generic_by_id[n].forward_table["ACN"] == "T"
assert ambiguous_generic_by_id[n].forward_table["GUU"] == "V"
assert ambiguous_generic_by_id[n].forward_table["GUN"] == "V"
if n != 23:
assert ambiguous_generic_by_id[n].forward_table["UUN"] == "X" # F or L
assert ambiguous_generic_by_id[n].forward_table["GTT"] == "V"
if n != 23:
assert ambiguous_generic_by_id[n].forward_table["TTN"] == "X" # F or L
assert ambiguous_generic_by_id[n].forward_table["GTN"] == "V"
# And finally something evil, an RNA-DNA mixture:
if n != 23:
assert ambiguous_generic_by_id[n].forward_table["UTN"] == "X" # F or L
assert ambiguous_generic_by_id[n].forward_table["UTU"] == "F"
# R = A or G, so URR = UAA or UGA / TRA = TAA or TGA = stop codons
if "UAA" in unambiguous_rna_by_id[n].stop_codons \
and "UGA" in unambiguous_rna_by_id[n].stop_codons:
try:
print(ambiguous_dna_by_id[n].forward_table["TRA"])
assert False, "Should be a stop only"
except KeyError:
pass
try:
print(ambiguous_rna_by_id[n].forward_table["URA"])
assert False, "Should be a stop only"
except KeyError:
pass
try:
print(ambiguous_generic_by_id[n].forward_table["URA"])
assert False, "Should be a stop only"
except KeyError:
pass
assert "URA" in ambiguous_generic_by_id[n].stop_codons
assert "URA" in ambiguous_rna_by_id[n].stop_codons
assert "TRA" in ambiguous_generic_by_id[n].stop_codons
assert "TRA" in ambiguous_dna_by_id[n].stop_codons
if "UAG" in unambiguous_rna_by_id[n].stop_codons \
and "UAA" in unambiguous_rna_by_id[n].stop_codons \
and "UGA" in unambiguous_rna_by_id[n].stop_codons:
try:
print(ambiguous_dna_by_id[n].forward_table["TAR"])
assert False, "Should be a stop only"
except KeyError:
pass
try:
print(ambiguous_rna_by_id[n].forward_table["UAR"])
assert False, "Should be a stop only"
except KeyError:
pass
try:
print(ambiguous_generic_by_id[n].forward_table["UAR"])
assert False, "Should be a stop only"
except KeyError:
pass
try:
print(ambiguous_generic_by_id[n].forward_table["URR"])
assert False, "Should be a stop OR an amino"
except TranslationError:
pass
assert "UAR" in ambiguous_generic_by_id[n].stop_codons
assert "UAR" in ambiguous_rna_by_id[n].stop_codons
assert "TAR" in ambiguous_generic_by_id[n].stop_codons
assert "TAR" in ambiguous_dna_by_id[n].stop_codons
assert "URA" in ambiguous_generic_by_id[n].stop_codons
assert "URA" in ambiguous_rna_by_id[n].stop_codons
assert "TRA" in ambiguous_generic_by_id[n].stop_codons
assert "TRA" in ambiguous_dna_by_id[n].stop_codons
if "UUG" in unambiguous_rna_by_id[n].start_codons \
and "CUG" in unambiguous_rna_by_id[n].start_codons \
and "AUG" in unambiguous_rna_by_id[n].start_codons \
and "UUG" not in unambiguous_rna_by_id[n].start_codons:
assert "NUG" not in ambiguous_dna_by_id[n].start_codons
assert "RUG" not in ambiguous_dna_by_id[n].start_codons
assert "WUG" not in ambiguous_dna_by_id[n].start_codons
assert "KUG" not in ambiguous_dna_by_id[n].start_codons
assert "SUG" not in ambiguous_dna_by_id[n].start_codons
assert "DUG" not in ambiguous_dna_by_id[n].start_codons
del n
# Table 2 Vertebrate Mitochondrial has
# TAA and TAG -> TAR, plus AGA and AGG -> AGR
assert "AGR" in ambiguous_dna_by_id[2].stop_codons
assert "TAR" in ambiguous_dna_by_id[2].stop_codons
assert "AGR" in ambiguous_rna_by_id[2].stop_codons
assert "UAR" in ambiguous_rna_by_id[2].stop_codons
assert "AGR" in ambiguous_generic_by_id[2].stop_codons
assert "UAR" in ambiguous_generic_by_id[2].stop_codons
assert "TAR" in ambiguous_generic_by_id[2].stop_codons
assert "UGA" not in ambiguous_rna_by_id[24].stop_codons
assert "UGA" not in ambiguous_rna_by_id[25].stop_codons
assert ambiguous_generic_by_id[1].stop_codons == ambiguous_generic_by_name["Standard"].stop_codons
assert ambiguous_generic_by_id[4].stop_codons == ambiguous_generic_by_name["SGC3"].stop_codons
assert ambiguous_generic_by_id[15].stop_codons == ambiguous_generic_by_name['Blepharisma Macronuclear'].stop_codons
assert ambiguous_generic_by_id[24].stop_codons == ambiguous_generic_by_name["Pterobranchia Mitochondrial"].stop_codons
assert ambiguous_generic_by_id[24].forward_table["AGA"] == "S" # Ser not Arg
assert ambiguous_generic_by_id[24].forward_table["AGG"] == "K" # Lys not Arg
assert ambiguous_generic_by_id[24].forward_table["UGA"] == "W" # Trp not stop
assert ambiguous_generic_by_id[25].forward_table["UGA"] == "G" # Gly not stop
assert ambiguous_generic_by_id[26].forward_table["CUG"] == "A" # Ala not Leu
print("Done")
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