# -*- coding: utf-8 -*- """ Created on Wed Dec 16 10:07:57 2015 @author: kurner, 4dsolutions (.net) (copyleft MIT license, 2015) Example: Rich Data Structures (for learning Python, including sqlite3) Source: http://www.soc-bdr.org/rds/authors/unit_tables_conversions_and_genetic_dicti... Any errors you discover in transcribing will be mine, please let me know and I'll correct my copy as well. kirby.urner@gmail.com Re: "Rich Data Structures" https://mail.python.org/pipermail/edu-sig/2006-June/006608.html (a more obvious need now that "big data" examples are in demand, for learning map/reduce techniques etc.). Indeed, we have many public raw data sets. A goal is to have some already in Python, as ready-to-go native data types. As here. This is not "big data", just data. Another experiment: https://mail.python.org/pipermail/edu-sig/2012-December/010709.html (same caveats about errors) """ amino_acid_abbrevs = \ dict( Phe = 'Phenyalinine', Leu = 'Leucine', Ser = 'Serine', Tyr = 'Tyrosine', Cys = 'Cysteine', Trp = 'Tryptophan', Pro = 'Proline', His = 'Histidine', Gln = 'Glutamine', Arg = 'Arginine', Ile = 'Isoleucine', Met = 'Methionine', Thr = 'Threonine', Asn = 'Asparagine', Lys = 'Lysine', Val = 'Valine', Ala = 'Alanine', Asp = 'Aspartate', Glu = 'Glutamate', Cly = 'Glycine') combos = [(a, b, c) for a in ('G','U','A','C') for b in ('G','U','A','C') for c in ('G','U','A','C')] # Also see: # https://flic.kr/p/BeVwN2 # (American Scientist Vol. 97) mRNA = \ { ('G', 'G', 'G') : 'Gly', ('G', 'G', 'U') : 'Gly', ('G', 'G', 'A') : 'Gly', ('G', 'G', 'C') : 'Gly', ('G', 'U', 'G') : 'Val', ('G', 'U', 'U') : 'Val', ('G', 'U', 'A') : 'Val', ('G', 'U', 'C') : 'Val', ('G', 'A', 'G') : 'Glu', ('G', 'A', 'U') : 'Asp', ('G', 'A', 'A') : 'Glu', ('G', 'A', 'C') : 'Asp', ('G', 'C', 'G') : 'Ala', ('G', 'C', 'U') : 'Ala', ('G', 'C', 'A') : 'Ala', ('G', 'C', 'C') : 'Ala', ('U', 'G', 'G') : 'Trp', ('U', 'G', 'U') : 'Cys', ('U', 'G', 'A') : 'STOP', ('U', 'G', 'C') : 'Cys', ('U', 'U', 'G') : 'Leu', ('U', 'U', 'U') : 'Phe', ('U', 'U', 'A') : 'Leu', ('U', 'U', 'C') : 'Phe', ('U', 'A', 'G') : 'STOP', ('U', 'A', 'U') : 'Tyr', ('U', 'A', 'A') : 'STOP', ('U', 'A', 'C') : 'Tyr', ('U', 'C', 'G') : 'Ser', ('U', 'C', 'U') : 'Ser', ('U', 'C', 'A') : 'Ser', ('U', 'C', 'C') : 'Ser', ('A', 'G', 'G') : 'Arg', ('A', 'G', 'U') : 'Ser', ('A', 'G', 'A') : 'Arg', ('A', 'G', 'C') : 'Ser', ('A', 'U', 'G') : 'Met', ('A', 'U', 'U') : 'Ile', ('A', 'U', 'A') : 'Ile', ('A', 'U', 'C') : 'Ile', ('A', 'A', 'G') : 'Lys', ('A', 'A', 'U') : 'Asn', ('A', 'A', 'A') : 'Lys', ('A', 'A', 'C') : 'Asn', ('A', 'C', 'G') : 'Thr', ('A', 'C', 'U') : 'Thr', ('A', 'C', 'A') : 'Thr', ('A', 'C', 'C') : 'Thr', ('C', 'G', 'G') : 'Arg', ('C', 'G', 'U') : 'Arg', ('C', 'G', 'A') : 'Arg', ('C', 'G', 'C') : 'Arg', ('C', 'U', 'G') : 'Leu', ('C', 'U', 'U') : 'Leu', ('C', 'U', 'A') : 'Leu', ('C', 'U', 'C') : 'Leu', ('C', 'A', 'G') : 'Gln', ('C', 'A', 'U') : 'His', ('C', 'A', 'A') : 'Gln', ('C', 'A', 'C') : 'His', ('C', 'C', 'G') : 'Pro', ('C', 'C', 'U') : 'Pro', ('C', 'C', 'A') : 'Pro', ('C', 'C', 'C') : 'Pro'} # [Ibid, www.soc-bdr.org] from Table 5. Genetic Code: # mRNA condon -> tRNA anti-codon # DNA column dropped (computable, replace mRNA U with T) # last column also not included. tRNA = \ { ('U','U','U'):(('A','A','A'), ('A','A','G')), ('U','U','C'):(('A','A','G'),), ('U','U','A'):(('A','A','U'),), ('U','U','G'):(('A','A','U'),('A','A','C')), ('U','C','U'):(('A','G','I'),('A','G','G'), ('A','G','A')), ('U','C','C'):(('A','G','I'),('A','G','G')), ('U','C','A'):(('A','G','I'),('A','G','U')), ('U','C','G'):(('A','G','C'),('A','G','U')), ('U','A','U'):(('A','U','A'),('A','U','G'),), ('U','A','C'):(('A','U','G'),), ('U','A','A'):(('A','U','U'),), ('U','A','G'):(('A','U','C'),('A','U','U')), ('U','G','U'):(('A','C','A'),('A','C','G')), ('U','G','C'):(('A','C','G'),), ('U','G','A'):(('A','C','U'),), ('U','G','G'):(('A','C','C'),), ('C','U','U'):(('G','A','I'),('G','A','G'),('G','A','A')), ('C','U','C'):(('G','A','I'),('G','A','G')), ('C','U','A'):(('G','A','I'),('G','A','U')), ('C','U','G'):(('G','A','C'),('G','A','U')), ('C','C','U'):(('G','G','I'),('G','G','G'),('G','G','A')), ('C','C','C'):(('G','G','I'),('G','G','G')), ('C','C','A'):(('G','G','I'),('G','G','U')), ('C','C','G'):(('G','G','C'),('G','G','U')), ('C','A','U'):(('G','U','A'),('G','U','G')), ('C','A','C'):(('G','U','G'),), ('C','A','A'):(('G','U','U'),), ('C','A','G'):(('G','U','C'),('G','U','U')), ('C','G','U'):(('G','C','I'),('G','C','G'),('G','C','A')), ('C','G','C'):(('G','C','I'),('G','C','G')), ('C','G','A'):(('G','C','I'),('G','C','U')), ('C','G','G'):(('G','C','C'),('G','C','U')), ('A','U','U'):(('U','A','I'),('U','A','G'),('U','A','A')), ('A','U','C'):(('U','A','I'),('U','A','G')), ('A','U','A'):(('U','A','I'),('U','A','U')), ('A','U','G'):(('U','A','C'),), ('A','C','U'):(('U','G','I'),('U','G','G'),('U','G','A')), ('A','C','C'):(('U','G','I'),('U','G','G')), ('A','C','A'):(('U','G','I'),('U','G','U')), ('A','C','G'):(('U','G','C'),('U','G','U')), ('A','A','U'):(('U','U','A'),('U','U','G')), ('A','A','C'):(('U','U','G'),), ('A','A','A'):(('U','U','U'),), ('A','A','G'):(('U','U','C'),('U','U','U')), ('A','G','U'):(('U','C','A'),('U','C','G')), ('A','G','C'):(('U','C','G'),), ('A','G','A'):(('U','C','U'),), ('A','G','G'):(('U','C','C'),('U','C','U')), ('G','U','U'):(('C','A','I'),('C','A','G'),('C','A','A')), ('G','U','C'):(('C','A','I'),('C','A','G')), ('G','U','A'):(('C','A','I'),('C','A','U')), ('G','U','G'):(('C','A','C'),('C','A','U')), ('G','C','U'):(('C','G','I'),('C','G','G'),('C','G','A')), ('G','C','C'):(('C','G','I'),('C','G','G')), ('G','C','A'):(('C','G','I'),('C','G','U')), ('G','C','G'):(('C','G','C'),('C','G','U')), ('G','A','U'):(('C','U','G'),('C','U','A')), ('G','A','C'):(('C','U','G'),), ('G','A','A'):(('C','U','U'),), ('G','A','G'):(('C','U','U'),('C','U','C')), ('G','G','U'):(('C','C','I'),('C','C','G'),('C','C','A')), ('G','G','C'):(('C','C','I'),('C','C','G')), ('G','G','A'):(('C','C','I'),('C','C','U')), ('G','G','G'):(('C','C','C'),('C','C','U')) }