--- /dev/null
+#!/usr/bin/env python
+#
+# Copyright (C) 2011 W. Trevor King <wking@drexel.edu>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program. If not, see
+# <http://www.gnu.org/licenses/>.
+
+AMINO_ACIDS = {
+ 'Alanine': ['Ala', 'A'],
+ 'Argenine': ['Arg', 'R'],
+ 'Asparagine': ['Asn', 'N'],
+ 'Aspartic acid': ['Asp', 'D'],
+ 'Cystine': ['Cys', 'C'],
+ 'Glutamic acid': ['Glu', 'E'],
+ 'Glutamine': ['Gln', 'Q'],
+ 'Glycine': ['Gly', 'G'],
+ 'Histidine': ['His', 'H'],
+ 'Isoleucine': ['Ile', 'I'],
+ 'Leucine': ['Leu', 'L'],
+ 'Lysine': ['Lys', 'K'],
+ 'Methionine': ['Met', 'M'],
+ 'Phenylalanine': ['Phe', 'F'],
+ 'Proline': ['Pro', 'P'],
+ 'Serine': ['Ser', 'S'],
+ 'Threonine': ['Thr', 'T'],
+ 'Tryptophan': ['Trp', 'W'],
+ 'Tyrosine': ['Tyr', 'Y'],
+ 'Valine': ['Val', 'V'],
+ }
+
+NUCLEOTIDES = {
+ 'Adenine': ['A'],
+ 'Cytosine': ['C'],
+ 'Guanine': ['G'],
+ 'Thymine': ['T'],
+ 'Uracil': ['U'],
+ }
+
+NUCLEOTIDE_COMPLEMENT = {
+ 'Adenine': 'Cytosine',
+ 'Cytosine': 'Adenine',
+ 'Guanine': 'Thymine',
+ 'Thymine': 'Guanine',
+ 'Uracil': 'Guanine',
+ }
+
+CODE = {
+ ('Adenine', 'Adenine', 'Adenine'): 'Lysine',
+ ('Adenine', 'Adenine', 'Cytosine'): 'Asparagine',
+ ('Adenine', 'Adenine', 'Guanine'): 'Lysine',
+ ('Adenine', 'Adenine', 'Uracil'): 'Asparagine',
+ ('Adenine', 'Cytosine', 'Adenine'): 'Threonine',
+ ('Adenine', 'Cytosine', 'Cytosine'): 'Threonine',
+ ('Adenine', 'Cytosine', 'Guanine'): 'Threonine',
+ ('Adenine', 'Cytosine', 'Uracil'): 'Threonine',
+ ('Adenine', 'Guanine', 'Adenine'): 'Argenine',
+ ('Adenine', 'Guanine', 'Cytosine'): 'Serine',
+ ('Adenine', 'Guanine', 'Guanine'): 'Argenine',
+ ('Adenine', 'Guanine', 'Uracil'): 'Serine',
+ ('Adenine', 'Uracil', 'Adenine'): 'Isoleucine',
+ ('Adenine', 'Uracil', 'Cytosine'): 'Isoleucine',
+ ('Adenine', 'Uracil', 'Guanine'): 'Methionine',
+ ('Adenine', 'Uracil', 'Uracil'): 'Isoleucine',
+ ('Cytosine', 'Adenine', 'Adenine'): 'Glutamine',
+ ('Cytosine', 'Adenine', 'Cytosine'): 'Histidine',
+ ('Cytosine', 'Adenine', 'Guanine'): 'Glutamine',
+ ('Cytosine', 'Adenine', 'Uracil'): 'Histidine',
+ ('Cytosine', 'Cytosine', 'Adenine'): 'Proline',
+ ('Cytosine', 'Cytosine', 'Cytosine'): 'Proline',
+ ('Cytosine', 'Cytosine', 'Guanine'): 'Proline',
+ ('Cytosine', 'Cytosine', 'Uracil'): 'Proline',
+ ('Cytosine', 'Guanine', 'Adenine'): 'Argenine',
+ ('Cytosine', 'Guanine', 'Cytosine'): 'Argenine',
+ ('Cytosine', 'Guanine', 'Guanine'): 'Argenine',
+ ('Cytosine', 'Guanine', 'Uracil'): 'Argenine',
+ ('Cytosine', 'Uracil', 'Adenine'): 'Leucine',
+ ('Cytosine', 'Uracil', 'Cytosine'): 'Leucine',
+ ('Cytosine', 'Uracil', 'Guanine'): 'Leucine',
+ ('Cytosine', 'Uracil', 'Uracil'): 'Leucine',
+ ('Guanine', 'Adenine', 'Adenine'): 'Glutamic acid',
+ ('Guanine', 'Adenine', 'Cytosine'): 'Aspartic acid',
+ ('Guanine', 'Adenine', 'Guanine'): 'Glutamic acid',
+ ('Guanine', 'Adenine', 'Uracil'): 'Aspartic acid',
+ ('Guanine', 'Cytosine', 'Adenine'): 'Alanine',
+ ('Guanine', 'Cytosine', 'Cytosine'): 'Alanine',
+ ('Guanine', 'Cytosine', 'Guanine'): 'Alanine',
+ ('Guanine', 'Cytosine', 'Uracil'): 'Alanine',
+ ('Guanine', 'Guanine', 'Adenine'): 'Glycine',
+ ('Guanine', 'Guanine', 'Cytosine'): 'Glycine',
+ ('Guanine', 'Guanine', 'Guanine'): 'Glycine',
+ ('Guanine', 'Guanine', 'Uracil'): 'Glycine',
+ ('Guanine', 'Uracil', 'Adenine'): 'Valine',
+ ('Guanine', 'Uracil', 'Cytosine'): 'Valine',
+ ('Guanine', 'Uracil', 'Guanine'): 'Valine',
+ ('Guanine', 'Uracil', 'Uracil'): 'Valine',
+ ('Uracil', 'Adenine', 'Adenine'): 'STOP (Ochre)',
+ ('Uracil', 'Adenine', 'Cytosine'): 'Tyrosine',
+ ('Uracil', 'Adenine', 'Guanine'): 'STOP (Amber)',
+ ('Uracil', 'Adenine', 'Uracil'): 'Tyrosine',
+ ('Uracil', 'Cytosine', 'Adenine'): 'Serine',
+ ('Uracil', 'Cytosine', 'Cytosine'): 'Serine',
+ ('Uracil', 'Cytosine', 'Guanine'): 'Serine',
+ ('Uracil', 'Cytosine', 'Uracil'): 'Serine',
+ ('Uracil', 'Guanine', 'Adenine'): 'STOP (Opal)',
+ ('Uracil', 'Guanine', 'Cytosine'): 'Cystine',
+ ('Uracil', 'Guanine', 'Guanine'): 'Tryptophan',
+ ('Uracil', 'Guanine', 'Uracil'): 'Cystine',
+ ('Uracil', 'Uracil', 'Adenine'): 'Leucine',
+ ('Uracil', 'Uracil', 'Cytosine'): 'Phenylalanine',
+ ('Uracil', 'Uracil', 'Guanine'): 'Leucine',
+ ('Uracil', 'Uracil', 'Uracil'): 'Phenylalanine',
+ }
+
+
+_INVERSE_DICTS = {}
+def unabbreviate(abbreviations, abbreviation):
+ """
+ >>> unabbreviate(AMINO_ACIDS, 'Ala')
+ 'Alanine'
+ >>> unabbreviate(AMINO_ACIDS, 'A')
+ 'Alanine'
+ >>> unabbreviate(NUCLEOTIDES, 'A')
+ 'Adenine'
+ """
+ try:
+ inverse = _INVERSE_DICTS[id(abbreviations)]
+ except KeyError:
+ inverse = {}
+ for k,abbrevs in abbreviations.items():
+ for abbrev in abbrevs:
+ inverse[abbrev] = k
+ _INVERSE_DICTS[id(abbreviations)] = inverse
+ inverse = _INVERSE_DICTS[id(abbreviations)]
+ return inverse[abbreviation]
+
+def decode_sequence(abbreviations, sequence):
+ """
+ >>> list(decode_sequence(NUCLEOTIDES, 'ACG TU'))
+ ['Adenine', 'Cytosine', 'Guanine', 'Thymine', 'Uracil']
+ """
+ for x in sequence:
+ if x.isspace():
+ continue
+ yield unabbreviate(abbreviations, x.upper())
+
+def transcribe_to_mRNA(nucleotides):
+ """
+ >>> list(transcribe_to_mRNA(['Adenine', 'Cytosine', 'Guanine', 'Thymine']))
+ ['Adenine', 'Cytosine', 'Guanine', 'Uracil']
+ """
+ for n in nucleotides:
+ if n == 'Thymine':
+ yield 'Uracil'
+ else:
+ yield n
+
+def split_into_codons(nucleotides, length=3):
+ """
+ >>> sequence = 'AGC TTC ATG CGT CCG AAG CC'
+ >>> nucleotides = decode_sequence(NUCLEOTIDES, sequence)
+ >>> codons = split_into_codons(nucleotides)
+ >>> print '\\n'.join(str(c) for c in codons)
+ ('Adenine', 'Guanine', 'Cytosine')
+ ('Thymine', 'Thymine', 'Cytosine')
+ ('Adenine', 'Thymine', 'Guanine')
+ ('Cytosine', 'Guanine', 'Thymine')
+ ('Cytosine', 'Cytosine', 'Guanine')
+ ('Adenine', 'Adenine', 'Guanine')
+ ('Cytosine', 'Cytosine')
+ """
+ codon = []
+ for n in nucleotides:
+ codon.append(n)
+ if len(codon) == length:
+ yield tuple(codon)
+ codon = []
+ if len(codon):
+ yield tuple(codon)
+
+def translate_to_amino_acids(nucleotides):
+ """
+ The input sequence should be mRNA nucleotides read from 5' to 3'.
+
+ >>> sequence = 'AUG AGC UUC AUG CGU CCG AAG'
+ >>> nucleotides = decode_sequence(NUCLEOTIDES, sequence)
+ >>> amino_acids = translate_to_amino_acids(nucleotides)
+ >>> print '\\n'.join(amino_acids)
+ Methionine
+ Serine
+ Phenylalanine
+ Methionine
+ Argenine
+ Proline
+ Lysine
+
+ The the leading Methionine is also the "start codon". There are
+ other possible start codon sequences (e.g. GUG) used in
+ prokaryotes such as E. coli.
+ """
+ for codon in split_into_codons(nucleotides):
+ aa = CODE[codon]
+ yield aa
+
+
+if __name__ == '__main__':
+ import argparse
+ import sys
+
+ p = argparse.ArgumentParser(
+ description='Translate DNA/mRNA to an amino acid sequence.')
+ p.add_argument(
+ 'sequence', metavar='ACGTU', nargs='*',
+ help="Genetic sequence to translate (5' to 3')")
+ p.add_argument(
+ '-s', '--short', action='store_true', default=False,
+ help='Use single-letter amino acid abbreviations')
+ p.add_argument(
+ '-m', '--match',
+ help='Match a protein sequence in the source mRNA')
+ p.add_argument(
+ '-c', '--complement', action='store_true', default=False,
+ help='Print the complement DNA amd exit')
+ p.add_argument(
+ '--count', action='store_true', default=False,
+ help='Print amino acid, nucleotide, and codon counts and exit')
+ p.add_argument(
+ '--table', action='store_true', default=False,
+ help='Print translation tables and exit')
+
+ args = p.parse_args()
+
+ if args.count:
+ print('amino acids: {:d}'.format(len(AMINO_ACIDS)))
+ print('nucleotides: {:d}'.format(len(NUCLEOTIDES)))
+ print('codons: {:d}'.format(len(CODE)))
+ sys.exit()
+ elif args.table:
+ print('RNA Amino acid')
+ print('=== ==========')
+ order = ('Uracil', 'Cytosine', 'Adenine', 'Guanine')
+ for x_ in order:
+ x = NUCLEOTIDES[x_][-1]
+ for y_ in order:
+ y = NUCLEOTIDES[y_][-1]
+ for z_ in order:
+ z = NUCLEOTIDES[z_][-1]
+ aa_ = CODE[(x_, y_, z_)]
+ try:
+ aa = ' '.join(AMINO_ACIDS[aa_])
+ except KeyError:
+ aa = aa_
+ print('{}{}{} {}'.format(x, y, z, aa))
+ print('')
+ print('AA RNA')
+ print('===== ===')
+ for aa_ in sorted(AMINO_ACIDS.keys()):
+ aa = ' '.join(AMINO_ACIDS[aa_])
+ codons = sorted(''.join(NUCLEOTIDES[x][-1] for x in k)
+ for k,v in CODE.items() if v == aa_)
+ print('{} {}'.format(aa, ' '.join(codons)))
+ sys.exit()
+
+ mRNA = ' '.join(args.sequence)
+ if args.complement:
+ for n in mRNA:
+ try:
+ nucleotide = unabbreviate(NUCLEOTIDES, n)
+ complement = NUCLEOTIDE_COMPLEMENT[nucleotide]
+ c = NUCLEOTIDES[complement][-1]
+ except KeyError:
+ c = n
+ sys.stdout.write(c)
+ sys.stdout.write('\n')
+ sys.exit()
+
+ nucleotides = decode_sequence(NUCLEOTIDES, mRNA)
+ nucleotides = list(transcribe_to_mRNA(nucleotides)) # no-op on mRNA
+ amino_acids = list(translate_to_amino_acids(nucleotides))
+
+ if args.match:
+ match = list(decode_sequence(AMINO_ACIDS, args.match))
+ for start in range(len(amino_acids)-len(match)):
+ fragment = amino_acids[start:start+len(match)]
+ if fragment == match:
+ start_n = start*3
+ stop_n = start_n + 3*len(match)
+ print('matched nucleotides {:d} through {:d}'.format(
+ start_n, stop_n-1))
+ print(''.join(NUCLEOTIDES[n][-1]
+ for n in nucleotides[start_n:stop_n]))
+ else:
+ if args.short:
+ sep = ''
+ i = -1
+ else:
+ sep = '-'
+ i = 0
+ print(sep.join(AMINO_ACIDS.get(aa, ['!'])[i] for aa in amino_acids))
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