def testReturnRightCodon(self):
"""
Must return the right codon.
"""
result = codonInformation(["GAT", "GAC"], ["GCC", "GCA"])
self.assertEqual([["GAC", "GCC"]], result[1])
self.assertEqual([["GAT", "GCC"], ["GAT", "GCA"], ["GAC", "GCA"]], result[2])
def testReturnRightCodon(self):
"""
Must return the right codon.
"""
result = codonInformation(['GAT', 'GAC'], ['GCC', 'GCA'])
self.assertEqual([['GAC', 'GCC']], result[1])
self.assertEqual([['GAT', 'GCC'], ['GAT', 'GCA'], ['GAC', 'GCA']],
result[2])
@return: An C{AminoAcid} instance, if one can be found. Else exit.
"""
aa = find(s)
if aa:
return aa
else:
print('Unknown amino acid or codon: %s' % s, file=sys.stderr)
print('Valid arguments are: %s.' % list(CODONS.keys()),
file=sys.stderr)
sys.exit(1)
if len(sys.argv) != 3:
print('Usage: %s amino_acid amino_acid' % sys.argv[0], file=sys.stderr)
sys.exit(1)
else:
aa1 = findOrDie(sys.argv[1])
aa2 = findOrDie(sys.argv[2])
distances = codonInformation(aa1.codons, aa2.codons)
print('Codons:')
print('%s: %s' % (aa1.name, ', '.join(sorted(aa1.codons))))
print('%s: %s' % (aa2.name, ', '.join(sorted(aa2.codons))))
print('Distances:')
sortedDistances = sorted(distances.keys())
for distance in sortedDistances:
for codon in distances[distance]:
print('%d: %s: %s -> %s: %s' %
(distance, aa1.name, codon[0], aa2.name, codon[1]))
@param s: A C{str} amino acid specifier. This may be a full name,
a 3-letter abbreviation or a 1-letter abbreviation. Case is ignored.
@return: An C{AminoAcid} instance, if one can be found. Else exit.
"""
aa = find(s)
if aa:
return aa
else:
print("Unknown amino acid or codon: %s" % s, file=sys.stderr)
print("Valid arguments are: %s." % list(CODONS.keys()), file=sys.stderr)
sys.exit(1)
if len(sys.argv) != 3:
print("Usage: %s amino_acid amino_acid" % sys.argv[0], file=sys.stderr)
sys.exit(1)
else:
aa1 = findOrDie(sys.argv[1])
aa2 = findOrDie(sys.argv[2])
distances = codonInformation(aa1.codons, aa2.codons)
print("Codons:")
print("%s: %s" % (aa1.name, ", ".join(sorted(aa1.codons))))
print("%s: %s" % (aa2.name, ", ".join(sorted(aa2.codons))))
print("Distances:")
sortedDistances = sorted(distances.keys())
for distance in sortedDistances:
for codon in distances[distance]:
print("%d: %s: %s -> %s: %s" % (distance, aa1.name, codon[0], aa2.name, codon[1]))
