KarrLab/intro_to_wc_modeling

""" Python exercise answers

:Author: Jonathan Karr <jonrkarr@gmail.com>
:Date: 2017-07-11
:Copyright: 2017, Karr Lab
:License: MIT
"""


def main():
    #########################################
    #########################################
    # a function which computes the volume of a spherical cell with radius 1 :math:`\mu m`
    import math

    def volume(radius):
        return 4 / 3 * math.pi * radius ** 3
    assert volume((3 / 4) ** (1 / 3)) == math.pi

    #########################################
    #########################################
    # Write a function which uses if statements to return the type of a codon (start, stop, other)

    def get_codon_type(codon):
        if codon in 'ATG':
            return 'start'
        elif codon in ['TAA', 'TAG', 'TGA']:
            return 'stop'
        else:
            return 'other'

    assert get_codon_type('ATG') == 'start'
    assert get_codon_type('TAG') == 'stop'
    assert get_codon_type('CTT') == 'other'

    #########################################
    #########################################
    # a class which represents RNA, with an attribute that stores the sequence
    # of each transcript and a method which uses a dictionary to compute the
    # amino acid sequence of the protein coded by the transcript

    class Rna(object):
        TRANSLATION_TABLE = {
            'TTT': 'F',
            'TTC': 'F',
            'TTA': 'L',
            'TTG': 'L',
            'CTT': 'L',
            'CTC': 'L',
            'CTA': 'L',
            'CTG': 'L',
            'ATT': 'I',
            'ATC': 'I',
            'ATA': 'I',
            'ATG': 'M',
            'GTT': 'V',
            'GTC': 'V',
            'GTA': 'V',
            'GTG': 'V',
            'TCT': 'S',
            'TCC': 'S',
            'TCA': 'S',
            'TCG': 'S',
            'CCT': 'P',
            'CCC': 'P',
            'CCA': 'P',
            'CCG': 'P',
            'ACT': 'T',
            'ACC': 'T',
            'ACA': 'T',
            'ACG': 'T',
            'GCT': 'A',
            'GCC': 'A',
            'GCA': 'A',
            'GCG': 'A',
            'TAT': 'Y',
            'TAC': 'Y',
            'TAA': '',
            'TAG': '',
            'CAT': 'H',
            'CAC': 'H',
            'CAA': 'Q',
            'CAG': 'Q',
            'AAT': 'N',
            'AAC': 'N',
            'AAA': 'K',
            'AAG': 'K',
            'GAT': 'D',
            'GAC': 'D',
            'GAA': 'E',
            'GAG': 'E',
            'TGT': 'C',
            'TGC': 'C',
            'TGA': '',
            'TGG': 'W',
            'CGT': 'R',
            'CGC': 'R',
            'CGA': 'R',
            'CGG': 'R',
            'AGT': 'S',
            'AGC': 'S',
            'AGA': 'R',
            'AGG': 'R',
            'GGT': 'G',
            'GGC': 'G',
            'GGA': 'G',
            'GGG': 'G',
        }

        def __init__(self, sequence):
            self.sequence = sequence

        def translate(self):
            aa_sequence = ''
            for position in range(int(len(self.sequence) / 3)):
                aa_sequence += self.TRANSLATION_TABLE[self.sequence[3 * position:3 * (position + 1)]]
            return aa_sequence

    assert Rna('ATGGTTACTGAACAT').translate() == 'MVTEH'

    #########################################
    #########################################
    # Import the ``csv`` package and use it to read a tab-separated file with
    # a header row into a list of dictionaries such as the example provided at
    # `https://en.wikipedia.org/wiki/Tab-separated_values
    # <https://en.wikipedia.org/wiki/Tab-separated_values>`_
    import os
    filename = os.path.join(os.path.dirname(__file__), '../../../docs/concepts_skills/software_engineering/example.tsv')
    with open(filename, 'w') as file:
        file.write(('Sepal length\tSepal width\tPetal length\tPetal width\tSpecies\n'
                    '5.1\t3.5\t1.4\t0.2\tI. setosa\n'
                    '4.9\t3.0\t1.4\t0.2\tI. setosa\n'
                    '4.7\t3.2\t1.3\t0.2\tI. setosa\n'
                    '4.6\t3.1\t1.5\t0.2\tI. setosa\n'
                    '5.0\t3.6\t1.4\t0.2\tI. setosa\n'))

    import csv
    with open(filename, 'r') as file:
        data = list(csv.DictReader(file, delimiter='\t'))

    assert len(data) == 5
    assert data[0] == {'Sepal length': '5.1', 'Sepal width': '3.5', 'Petal length': '1.4', 'Petal width': '0.2', 'Species': 'I. setosa'}

    os.remove(filename)

    #########################################
    #########################################
    # Use the ``print`` and ``format`` methods to write `Hello {your name}!` to standard out
    import abduct
    with abduct.captured(abduct.out(tee=True)) as stdout:
        print('Hello {}'.format('reader'))
        out_text = stdout.getvalue()

    # assert stdout == 'Hello reader' # this causes an error in Read the Docs