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Format; use google docstring format; fix docstring typos #2

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Format; use google docstring format; fix docstring typos #2

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221 changes: 194 additions & 27 deletions amino_acids.py
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@@ -1,31 +1,198 @@
aa = ['F', 'L', 'I', 'M', 'V', 'S', 'P', 'T', 'A', 'Y',
'|', 'H', 'Q', 'N', 'K', 'D', 'E', 'C', 'W', 'R',
'G']

codons = [['TTT', 'TTC'],
['TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG'],
['ATT', 'ATC', 'ATA'],
['ATG'],
['GTT', 'GTC', 'GTA', 'GTG'],
['TCT', 'TCC', 'TCA', 'TCG', 'AGT', 'AGC'],
['CCT', 'CCC', 'CCA', 'CCG'],
['ACT', 'ACC', 'ACA', 'ACG'],
['GCT', 'GCC', 'GCA', 'GCG'],
['TAT', 'TAC'],
['TAA', 'TAG', 'TGA'],
['CAT', 'CAC'],
['CAA', 'CAG'],
['AAT', 'AAC'],
['AAA', 'AAG'],
['GAT', 'GAC'],
['GAA', 'GAG'],
['TGT', 'TGC'],
['TGG'],
['CGT', 'CGC', 'CGA', 'CGG', 'AGA', 'AGG'],
['GGT', 'GGC', 'GGA', 'GGG']]
"""
This module maps codons to amino acids.

Attributes:
aa_table (dict(str, str)):
A map from codons to amino acids. Codons are represented as strings
in IUPAC notation, e.g. 'TTT'. Amino acids are represented by their
single-letter IUPAC nucleobase abbreviations, e.g. 'F' for
phenylalanine.

Examples:

>>> aa_table['TTC']
'F'
>>> aa_table['TTA']
'L'
>>> aa_table['GGA']
'G'

References:
* DNA codon table: https://en.wikipedia.org/wiki/DNA_codon_table
* IUPAC notation: https://en.wikipedia.org/wiki/Nucleic_acid_notation

"""

# amino acids, in the same order as in `codons`. This is used to construct
# `aa_table`.
amino_acids = [
'F', 'L', 'I', 'M', 'V', 'S', 'P', 'T', 'A', 'Y', '|', 'H', 'Q', 'N', 'K',
'D', 'E', 'C', 'W', 'R', 'G']

# A list of lists of codons, in the same order as `amino_acids`.
codons = [
['TTT', 'TTC'],
['TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG'],
['ATT', 'ATC', 'ATA'],
['ATG'],
['GTT', 'GTC', 'GTA', 'GTG'],
['TCT', 'TCC', 'TCA', 'TCG', 'AGT', 'AGC'],
['CCT', 'CCC', 'CCA', 'CCG'],
['ACT', 'ACC', 'ACA', 'ACG'],
['GCT', 'GCC', 'GCA', 'GCG'],
['TAT', 'TAC'],
['TAA', 'TAG', 'TGA'],
['CAT', 'CAC'],
['CAA', 'CAG'],
['AAT', 'AAC'],
['AAA', 'AAG'],
['GAT', 'GAC'],
['GAA', 'GAG'],
['TGT', 'TGC'],
['TGG'],
['CGT', 'CGC', 'CGA', 'CGG', 'AGA', 'AGG'],
['GGT', 'GGC', 'GGA', 'GGG']
]

# create a dictionary lookup table for mapping codons into amino acids
# See Think Python Ch. 11
# http://greenteapress.com/thinkpython/html/thinkpython012.html
# http://greenteapress.com/thinkpython/html/thinkpython012.html
aa_table = {}
for i in range(len(aa)):
for i in range(len(amino_acids)):
for codon in codons[i]:
aa_table[codon] = aa[i]
aa_table[codon] = amino_acids[i]

# Use `enumerate` to avoid having to compute the size of the list,
# and then select each of its items as a separate operation.
# `enumerate` produces a sequence of (index, item) pairs that
# `i` and `nucleotide_codons` bind to.
# See: https://docs.python.org/3/library/functions.html#enumerate
aa_table = {}
for i, nucleotide_codons in enumerate(codons):
for codon in nucleotide_codons:
aa_table[codon] = amino_acids[i]

# `zip` produces a sequence of pairs: a pair that contains the first item from
# each of `codons` and `amino_acids`, then the second item from each, and so
# on.
# See: https://docs.python.org/3/library/functions.html#zip
aa_table = {}
for nucleotide_codons, amino_acid in zip(codons, amino_acids):
for codon in nucleotide_codons:
aa_table[codon] = amino_acid

# instead of creating an empty dictionary and then filling it, use a
# dictionary comprehension to create the dictionary in one swell foop.
aa_table = {codon: aa
for aa_codons, aa in zip(codons, amino_acids)
for codon in aa_codons}

# instead of including `codons` and `amino_acids` as above, read
# the map from a CSV ("commma-separated values") file.
# The file looks like this:
# AAA,K
# AAC,N
# AAG,K
# etc.
aa_table = dict(line.strip().split(',')
for line in open('codon_nucleotides.csv').readlines())



def fn(a, b):
if test():
return


#!/usr/bin/env python3


# The Pandas library can read CSV and Excel tables, and manipulate tables
# within a Python program. It's overkill for this purpose, but
import doctest

# very powerful in general.
# See: http://pandas.pydata.org
import pandas as pd

aa_table = pd.read_csv('codon_nucleotides.csv', header=None, index_col=0)[1]

# The previous solution, unlike all the others, doesn't actually create
# a Python dict. It creates a (Pandas) Series, which can be used the same
aa_table = dict(pd.read_csv('codon_nucleotides.csv',
header=None, index_col=0)[1])
# do this instead:
aa_table = dict(pd.read_csv('codon_nucleotides.csv',
header=None, index_col=0)[1])

# Finally, we could just list out the key-value pairs in the dictionary.
aa_table = {
'AAA': 'K',
'AAC': 'N',
'AAG': 'K',
'AAT': 'N',
'ACA': 'T',
'ACC': 'T',
'ACG': 'T',
'ACT': 'T',
'AGA': 'R',
'AGC': 'S',
'AGG': 'R',
'AGT': 'S',
'ATA': 'I',
'ATC': 'I',
'ATG': 'M',
'ATT': 'I',
'CAA': 'Q',
'CAC': 'H',
'CAG': 'Q',
'CAT': 'H',
'CCA': 'P',
'CCC': 'P',
'CCG': 'P',
'CCT': 'P',
'CGA': 'R',
'CGC': 'R',
'CGG': 'R',
'CGT': 'R',
'CTA': 'L',
'CTC': 'L',
'CTG': 'L',
'CTT': 'L',
'GAA': 'E',
'GAC': 'D',
'GAG': 'E',
'GAT': 'D',
'GCA': 'A',
'GCC': 'A',
'GCG': 'A',
'GCT': 'A',
'GGA': 'G',
'GGC': 'G',
'GGG': 'G',
'GGT': 'G',
'GTA': 'V',
'GTC': 'V',
'GTG': 'V',
'GTT': 'V',
'TAA': '|',
'TAC': 'Y',
'TAG': '|',
'TAT': 'Y',
'TCA': 'S',
'TCC': 'S',
'TCG': 'S',
'TCT': 'S',
'TGA': '|',
'TGC': 'C',
'TGG': 'W',
'TGT': 'C',
'TTA': 'L',
}
'TTG': 'L',
'TTT': 'F'
}


doctest.testmod()