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‎extra/03_dna/Makefile‎

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.PHONY: test pdf
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pdf:
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asciidoctor-pdf -o README.pdf README.adoc
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test:
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pytest -xv test.py

‎extra/03_dna/README.adoc‎

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= Counting DNA Nucleotides
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In this exercise, we'll count the frequency of the four nucleotide bases in a given string of DNA as described on the http://rosalind.info/problems/dna/[Rosalind.info site]footnote:[This is a website with various bioinformatics coding challenges. It's named after Rosalind Franklin who should have gotten a Nobel Prize for her work on discovering the double-helix structure of DNA. Instead, she died early with little recognition of her contributions, but she did get this website named after her.]
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Write a Python program called `dna.py` that will accept a single, required, positional argument that is a string of `dna` and print the number of times you see each of the bases A, C, G, and T (in that order) separated by spaces.
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The program should print a brief usage when run with no input:
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----
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$ ./dna.py
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usage: dna.py [-h] str
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dna.py: error: the following arguments are required: str
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----
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Or a longer usage for the `-h` or `--help` flags:
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----
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$ ./dna.py -h
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usage: dna.py [-h] str
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Count DNA nucleotides
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positional arguments:
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str DNA
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optional arguments:
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-h, --help show this help message and exit
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----
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Examples of running:
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----
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$ ./dna.py A
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1 0 0 0
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$ ./dna.py C
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0 1 0 0
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$ ./dna.py G
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0 0 1 0
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$ ./dna.py T
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0 0 0 1
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$ ./dna.py AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
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20 12 17 21
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----
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A passing test suite looks like this:
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----
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$ make test
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pytest -xv test.py
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============================= test session starts ==============================
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...
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collected 11 items
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test.py::test_exists PASSED [ 9%]
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test.py::test_no_arg_and_usage PASSED [ 18%]
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test.py::test_a_upper PASSED [ 27%]
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test.py::test_a_lower PASSED [ 36%]
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test.py::test_c_upper PASSED [ 45%]
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test.py::test_c_lower PASSED [ 54%]
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test.py::test_g_upper PASSED [ 63%]
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test.py::test_g_lower PASSED [ 72%]
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test.py::test_t_upper PASSED [ 81%]
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test.py::test_t_lower PASSED [ 90%]
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test.py::test_rosalind_example PASSED [100%]
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============================== 11 passed in 0.61s ==============================
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----
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NOTE: Solve this problem using only the skills you've learned up to chapter 3 -- that is, only using Python `str` methods.

‎extra/03_dna/README.pdf‎

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‎extra/03_dna/test.py‎

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#!/usr/bin/env python3
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"""tests for dna.py"""
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import os
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import random
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import re
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import string
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from subprocess import getstatusoutput, getoutput
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prg = './dna.py'
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# --------------------------------------------------
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def test_exists():
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"""exists"""
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assert os.path.isfile(prg)
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# --------------------------------------------------
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def test_no_arg_and_usage():
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"""usage"""
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for flag in ['', '-h', '--help']:
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out = getoutput(f'{prg} {flag}')
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assert out.lower().startswith('usage')
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# --------------------------------------------------
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def run_single(base):
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"""Run a single base test"""
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num = random.randint(1, 10)
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given = base * num
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rv, out = getstatusoutput(f'{prg} {given}')
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assert rv == 0
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cmp = base.upper()
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expected = f'{num} 0 0 0' if cmp == 'A' else \
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f'0 {num} 0 0' if cmp == 'C' else \
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f'0 0 {num} 0' if cmp == 'G' else \
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f'0 0 0 {num}'
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assert out == expected
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# --------------------------------------------------
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def test_a_upper():
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"""A"""
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run_single('A')
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# --------------------------------------------------
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def test_a_lower():
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"""a"""
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run_single('a')
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# --------------------------------------------------
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def test_c_upper():
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"""C"""
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run_single('C')
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# --------------------------------------------------
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def test_c_lower():
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"""c"""
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run_single('c')
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# --------------------------------------------------
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def test_g_upper():
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"""G"""
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run_single('G')
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# --------------------------------------------------
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def test_g_lower():
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"""g"""
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run_single('g')
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# --------------------------------------------------
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def test_t_upper():
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"""T"""
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run_single('T')
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# --------------------------------------------------
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def test_t_lower():
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"""t"""
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run_single('t')
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# --------------------------------------------------
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def test_rosalind_example():
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"""From http://rosalind.info/problems/dna/"""
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dna = ('AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATT'
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'AAAAAAAGAGTGTCTGATAGCAGC')
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rv, out = getstatusoutput(f'{prg} {dna}')
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assert rv == 0
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assert out == '20 12 17 21'

‎extra/03_strings/Makefile‎

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.PHONY: test pdf
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pdf:
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asciidoctor-pdf -o README.pdf README.adoc
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test:
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pytest -xv test.py

‎extra/03_strings/README.adoc‎

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= Text Classifier
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Write a Python program called `classify.py` that will report if a given input is:
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* uppercase, e.g., "HELLO"
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* lowercase, e.g., "hello"
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* title case, e.g., "Hello"
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* a digit, e.g., "10"
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* a space, e.g., " " or the tab character "\t"
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* none of the above, e.g., "1.2"
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The program should work like so:
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----
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$ ./classify.py HELLO
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HELLO is uppercase.
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$ ./classify.py hello
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hello is lowercase.
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$ ./classify.py Hello
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Hello is title case.
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$ ./classify.py 10
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10 is a digit.
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$ ./classify.py " "
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input is space.
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$ ./classify.py "1.2"
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1.2 is unclassified.
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----
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It should print a brief usage if provided with no arguments:
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----
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$ ./classify.py
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usage: classify.py [-h] str
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classify.py: error: the following arguments are required: str
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----
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And a longer usage for the `-h` or `--help` flags:
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----
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$ ./classify.py -h
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usage: classify.py [-h] str
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Classify a given string
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positional arguments:
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str Some text
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optional arguments:
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-h, --help show this help message and exit
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----
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It should pass all the tests:
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----
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$ make test
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pytest -xv test.py
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============================= test session starts ==============================
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...
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collected 8 items
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test.py::test_exists PASSED [ 12%]
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test.py::test_usage PASSED [ 25%]
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test.py::test_upper PASSED [ 37%]
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test.py::test_lower PASSED [ 50%]
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test.py::test_title PASSED [ 62%]
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test.py::test_digit PASSED [ 75%]
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test.py::test_space PASSED [ 87%]
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test.py::test_unclassified PASSED [100%]
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============================== 8 passed in 0.44s ===============================
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----

‎extra/03_strings/README.pdf‎

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‎extra/03_strings/test.py‎

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#!/usr/bin/env python3
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"""tests for classify.py"""
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import os
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import random
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import re
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import string
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from subprocess import getstatusoutput
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prg = './classify.py'
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# --------------------------------------------------
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def test_exists():
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"""exists"""
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assert os.path.isfile(prg)
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# --------------------------------------------------
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def test_usage():
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"""usage"""
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for flag in ['-h', '--help']:
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rv, out = getstatusoutput(f'{prg} {flag}')
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assert rv == 0
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assert out.lower().startswith('usage')
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# --------------------------------------------------
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def test_upper():
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"""upper"""
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word = random.choice('APPLE BANANA CHERRY'.split())
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rv, out = getstatusoutput(f'{prg} {word}')
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assert rv == 0
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assert out == f'{word} is uppercase.'
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# --------------------------------------------------
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def test_lower():
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"""lower"""
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word = random.choice('apple banana cherry'.split())
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rv, out = getstatusoutput(f'{prg} {word}')
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assert rv == 0
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assert out == f'{word} is lowercase.'
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# --------------------------------------------------
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def test_title():
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"""title"""
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word = random.choice('Apple Banana Cherry'.split())
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rv, out = getstatusoutput(f'{prg} {word}')
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assert rv == 0
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assert out == f'{word} is title case.'
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# --------------------------------------------------
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def test_digit():
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"""digit"""
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word = random.choice('1 2 3'.split())
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rv, out = getstatusoutput(f'{prg} {word}')
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assert rv == 0
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assert out == f'{word} is a digit.'
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# --------------------------------------------------
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def test_space():
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"""space"""
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word = random.choice([' ', '\t'])
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rv, out = getstatusoutput(f'{prg} "{word}"')
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assert rv == 0
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assert out == f'input is space.'
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# --------------------------------------------------
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def test_unclassified():
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"""unclassified"""
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word = random.choice('1.2 3.04 40.5'.split())
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rv, out = getstatusoutput(f'{prg} "{word}"')
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assert rv == 0
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assert out == f'{word} is unclassified.'

‎extra/Makefile‎

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clean:
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find . -name __pycache__ -o -name .pytest_cache -o -name .mypy_cache -exec rm -rf {} \;

‎extra/README.md‎

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# Extras
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These are additional coding challenges for which I will not provide solutions, only tests. Good luck!

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