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‎.gitignore‎

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.log
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.coverage
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.idea
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.vscode

‎extra/08_rna/Makefile‎

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.PHONY: test pdf clean
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pdf:
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asciidoctor-pdf README.adoc
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test:
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pytest -xv test.py
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clean:
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rm -rf __pycache__

‎extra/08_rna/README.adoc‎

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# Transcribing DNA into RNA
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For this exercise, we'll be applying what we learned about modifying strings to a variation on this Rosalind exercise that transcribes DNA into RNA:
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http://rosalind.info/problems/rna/
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You will write a Python program called `transcribe.py` that will accept:
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* One or more positional arguments which must be readable files
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* An optional `-o` or `--outdir` argument that names an output directory (default `'out'`)
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You can use the `os.path.isdir` to check if the output directory exists.
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It works just like the `os.path.isfile` function we've used that will return `True` or `False` if a given string names an existing file, only this checks for a directory.
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Here assuming that "blargh" does not exist on your system:
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----
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>>> import os
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>>> os.path.isdir('blargh')
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False
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----
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If the directory does not exist, you should use the `os.makedirs` function to create it.
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Here is a bit of code you can put into your program:
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----
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if not os.path.isdir(out_dir):
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os.makedirs(out_dir)
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----
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Your program will read each of the input files which will contain a single DNA sequence on each line.
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The sequences will need to replace the `T` bases with `U`.
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For instance, the `input1.txt` file contains a single sequence `'GATGGAACTTGACTACGTAAATT'` which will become `'GAUGGAACUUGACUACGUAAAUU'`.
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The new sequences from each input file will be written to a new output file in the `--outdir`.
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The name of the file will be the "basename" of the input file which you can get by using the `os.path.basename` function.
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For instance, the "basename" of `'./inputs/input1.txt'` is `'input1.txt'`:
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----
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>>> base = os.path.basename('./inputs/input1.txt')
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>>> base
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'input1.txt'
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----
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If the output directory is `'out'`, you can create a new path for the output file by using the `os.path.join` function with the basename of the input file's basename:
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----
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>>> out_dir = 'out'
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>>> os.path.join(out_dir, base)
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'out/input1.txt'
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----
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If you declare your `args.file` parameter using `type=argparse.FileType('r')`, then you'll be iterating over a list of _open file handles_.
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You can use the `fh.name` to get the name of the file:
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----
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for fh in args.file:
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out_file = os.path.join(out_dir, os.path.basename(fh.name))
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out_fh = open(out_file, 'wt')
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----
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You will have two levels of iteration:
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* Each `file` argument
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* Each line in each file
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You will need to `open` the output file for writing text, iterate over each line in the input file, and print the transcribed sequences to the output file.
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Your program should print a brief usage when given no arguments:
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----
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$ ./transcribe.py
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usage: transcribe.py [-h] [-o DIR] FILE [FILE ...]
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transcribe.py: error: the following arguments are required: FILE
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----
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And a longer usage for `-h` and `--help`:
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----
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$ ./transcribe.py -h
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usage: transcribe.py [-h] [-o DIR] FILE [FILE ...]
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Transcribing DNA into RNA
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positional arguments:
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FILE Input file(s)
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optional arguments:
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-h, --help show this help message and exit
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-o DIR, --outdir DIR Output directory (default: out)
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----
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The output from the program should summarize how many sequences and files were processed.
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For example, the `input1.txt` file contains a single line/sequence, so the result should be this:
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----
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$ ./transcribe.py inputs/input1.txt
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Done, wrote 1 sequence in 1 file to directory "out".
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----
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While the `input2.txt` file contains two lines/sequences:
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----
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$ ./transcribe.py inputs/input2.txt
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Done, wrote 2 sequences in 1 file to directory "out".
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----
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When you process both together, it should summarize for all the inputs:
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----
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$ ./transcribe.py inputs/*
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Done, wrote 3 sequences in 2 files to directory "out".
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----
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Note that you must use the correct singular/plural for both "sequence(s)" and "file(s)."
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Many elements of this program are almost identical to the `wc.py` program, so I would recommend you revisit that.
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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 7 items
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test.py::test_exists PASSED [ 14%]
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test.py::test_usage PASSED [ 28%]
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test.py::test_no_args PASSED [ 42%]
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test.py::test_bad_file PASSED [ 57%]
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test.py::test_good_input1 PASSED [ 71%]
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test.py::test_good_input2 PASSED [ 85%]
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test.py::test_good_multiple_inputs PASSED [100%]
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============================== 7 passed in 0.36s ===============================
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----

‎extra/08_rna/README.pdf‎

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‎extra/08_rna/inputs/input1.txt‎

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GATGGAACTTGACTACGTAAATT

‎extra/08_rna/inputs/input2.txt‎

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CTTAGGTCAGTGGTCTCTAAACTTTCGGTTCTGTCGTCTTCATAGGCAAATTTTTGAACCGGCAGACAAGCTAATCCCTGTGCGGTTAGCTCAAGCAACAGAATGTCCGATCTTTGAACTTCCTAACGAACCGAACCTACTATAATTACATACGAATAATGTATGGGCTAGCGTTGGCTCATCATCAAGTCTGCGGTGAAATGGGAACATATTCGCATTGCATATAGGGCGTATCTGACGATCGATTCGAGTTGGCTAGTCGTACCAAATGATTATGGGCTGGAGGGCCAATGTATACGTCAGCCAGGCTAAACCACTGGACCGCTTGCAATCCATAGGAAGTAAAATTACCCTTTTTAAACTCTCTAAGATGTGGCGTCTCGTTCTTAAGGAGTAATGAGACTGTGACAACATTGGCAAGCACAGCCTCAGTATAGCTACAGCACCGGTGCTAATAGTAAATGCAAACACCGTTTCAAGAGCCGAGCCTTTTTTTAATGCAAGGTGACTTCAGAGGGAGTAAATCGTGGCCGGGGACTGTCCAGAGCAATGCATTCCCGAGTGCGGGTACCCGTGGTGTGAGAGGAATCGATTTCGCGTGTGATACCATTAATGGTCCTGTACTACTGTCAGTCAGCTTGATTTGAAGTCGGCCGACAAGGTTGGTACATAATGGGCTTACTGGGAGCTTAGGTTAGCCTCTGGAAAACTTTAGAATTTATATGGGTGTTTCTGTGTTCGTACAGGCCCCAGTCGGGCCATCGTTGTTGAGCATAGACCGGTGTAACCTTAATTATTCACAGGCCAATCCCCGTATACGCATCTGAAAGGCACACCGCCTATTACCAATTTGCGCTTCCTTACATAGGAGGACCTGTTATCGTCTTCTCAATCGCTGAGTTACCTTAAAACTAGGATC
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ACCGAGTAAAAGGCGACGGTTCGTTTCCGAACCTATTTGCTCTTATTTCTACGGGCTGCTAGTGTTGTAGGCTGCAAAACCTACGTAGTCCCATCTATCATGCTCGACCCTACGAGGCTAATGTCTTGTCAGAGGCCCGTCATGTGCCACGTACATACACCAATGTATACCGCTCTAGCGGTTTGGTGTAGTAGGACTTGTGTATGCACGCTACAGCGAACAACGTTGATCCCTAACTGAAGTCGGGCTCCGCAGGCCTACTCACGCCGTTTCTATAGGTTGAGCCGCATCAAACATTGGGTTGAGTCTCGAGTATAGAGGAAGGCTCTGGTGGCAGGCGCGACGTTGATCGGGAGGAGTATGGATGGTGATCAATCCCCGTGCCAATCGCGAGTACTACAGGAGGAGGGGGCGGCTCTGTTCAATCATCACCCGTTCCATCACACGGGCAGCACAGTTGACCTCCCGAGCCGTCTCACGGACCTAGTGGCAACAGGTGTATTGAAGCGCCGGGAATAGTCATACCCGTGGGCTTGATTGAGAGACCGAAATTCCGACCGCCAAAACTGCTGATATCGTACGCCTTACTACAAAACAAATGACGTCACTACCGGCCAGGGACAAGCTTATTAATTAAGTAGGAACCCTATACCTTGCACATCCTAAATCTAGCAGCGGGTCCAGGATTGGTTCCAGTCCAACGCGCGATGCGCGTCAAGCTAGGCGAATGACCACGGTCGAAACACCACTTATGTGACCCACCTTGGCCAACTCTCCCGATTCTCCTCGCTACTATCTTGAAGGTCACTGAGAATATCCCTTATGGGTCGCATACGGAGACAGCCGCAGGAGCCTTAACGGAGAATACGCCAATACTATGTTCTGGGTCGGTGGGTGTAATGCGATGCAATCCGATCGTGCGAACGTTCCCTTTGATGACTATAGGGTCTAGTGATCGTACATGTGC

‎extra/08_rna/test.py‎

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#!/usr/bin/env python3
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"""tests for transcribe.py"""
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from subprocess import getstatusoutput
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import os.path
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import re
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import string
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import random
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from shutil import rmtree
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prg = './transcribe.py'
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input1 = './inputs/input1.txt'
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input2 = './inputs/input2.txt'
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# --------------------------------------------------
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def random_filename():
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"""generate a random filename"""
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return ''.join(random.choices(string.ascii_uppercase + string.digits, k=5))
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# --------------------------------------------------
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def test_exists():
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"""usage"""
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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('{} {}'.format(prg, flag))
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assert rv == 0
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assert re.match("usage", out, re.IGNORECASE)
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# --------------------------------------------------
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def test_no_args():
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"""die on no args"""
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rv, out = getstatusoutput(prg)
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assert rv != 0
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assert re.match("usage", out, re.IGNORECASE)
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# --------------------------------------------------
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def test_bad_file():
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"""die on missing input"""
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bad = random_filename()
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rv, out = getstatusoutput(f'{prg} {bad}')
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assert rv != 0
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assert re.match('usage:', out, re.I)
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assert re.search(f"No such file or directory: '{bad}'", out)
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# --------------------------------------------------
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def test_good_input1():
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"""runs on good input"""
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out_dir = 'out'
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try:
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if os.path.isdir(out_dir):
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rmtree(out_dir)
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rv, out = getstatusoutput(f'{prg} {input1}')
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assert rv == 0
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assert out == 'Done, wrote 1 sequence in 1 file to directory "out".'
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assert os.path.isdir(out_dir)
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out_file = os.path.join(out_dir, 'input1.txt')
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assert os.path.isfile(out_file)
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assert open(out_file).read().rstrip() == 'GAUGGAACUUGACUACGUAAAUU'
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finally:
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if os.path.isdir(out_dir):
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rmtree(out_dir)
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# --------------------------------------------------
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def test_good_input2():
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"""runs on good input"""
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out_dir = random_filename()
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try:
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if os.path.isdir(out_dir):
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rmtree(out_dir)
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rv, out = getstatusoutput(f'{prg} -o {out_dir} {input2}')
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assert rv == 0
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assert out == f'Done, wrote 2 sequences in 1 file to directory "{out_dir}".'
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assert os.path.isdir(out_dir)
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out_file = os.path.join(out_dir, 'input2.txt')
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assert os.path.isfile(out_file)
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assert open(out_file).read().rstrip() == output2().rstrip()
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finally:
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if os.path.isdir(out_dir):
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rmtree(out_dir)
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# --------------------------------------------------
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def test_good_multiple_inputs():
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"""runs on good input"""
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out_dir = random_filename()
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try:
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if os.path.isdir(out_dir):
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rmtree(out_dir)
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rv, out = getstatusoutput(f'{prg} --outdir {out_dir} {input1} {input2}')
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assert rv == 0
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assert out == f'Done, wrote 3 sequences in 2 files to directory "{out_dir}".'
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assert os.path.isdir(out_dir)
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out_file1 = os.path.join(out_dir, 'input1.txt')
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out_file2 = os.path.join(out_dir, 'input2.txt')
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assert os.path.isfile(out_file1)
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assert os.path.isfile(out_file2)
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assert open(out_file1).read().rstrip() == 'GAUGGAACUUGACUACGUAAAUU'
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assert open(out_file2).read().rstrip() == output2().rstrip()
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finally:
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if os.path.isdir(out_dir):
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rmtree(out_dir)
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# --------------------------------------------------
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def output2():
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return """CUUAGGUCAGUGGUCUCUAAACUUUCGGUUCUGUCGUCUUCAUAGGCAAAUUUUUGAACCGGCAGACAAGCUAAUCCCUGUGCGGUUAGCUCAAGCAACAGAAUGUCCGAUCUUUGAACUUCCUAACGAACCGAACCUACUAUAAUUACAUACGAAUAAUGUAUGGGCUAGCGUUGGCUCAUCAUCAAGUCUGCGGUGAAAUGGGAACAUAUUCGCAUUGCAUAUAGGGCGUAUCUGACGAUCGAUUCGAGUUGGCUAGUCGUACCAAAUGAUUAUGGGCUGGAGGGCCAAUGUAUACGUCAGCCAGGCUAAACCACUGGACCGCUUGCAAUCCAUAGGAAGUAAAAUUACCCUUUUUAAACUCUCUAAGAUGUGGCGUCUCGUUCUUAAGGAGUAAUGAGACUGUGACAACAUUGGCAAGCACAGCCUCAGUAUAGCUACAGCACCGGUGCUAAUAGUAAAUGCAAACACCGUUUCAAGAGCCGAGCCUUUUUUUAAUGCAAGGUGACUUCAGAGGGAGUAAAUCGUGGCCGGGGACUGUCCAGAGCAAUGCAUUCCCGAGUGCGGGUACCCGUGGUGUGAGAGGAAUCGAUUUCGCGUGUGAUACCAUUAAUGGUCCUGUACUACUGUCAGUCAGCUUGAUUUGAAGUCGGCCGACAAGGUUGGUACAUAAUGGGCUUACUGGGAGCUUAGGUUAGCCUCUGGAAAACUUUAGAAUUUAUAUGGGUGUUUCUGUGUUCGUACAGGCCCCAGUCGGGCCAUCGUUGUUGAGCAUAGACCGGUGUAACCUUAAUUAUUCACAGGCCAAUCCCCGUAUACGCAUCUGAAAGGCACACCGCCUAUUACCAAUUUGCGCUUCCUUACAUAGGAGGACCUGUUAUCGUCUUCUCAAUCGCUGAGUUACCUUAAAACUAGGAUC
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ACCGAGUAAAAGGCGACGGUUCGUUUCCGAACCUAUUUGCUCUUAUUUCUACGGGCUGCUAGUGUUGUAGGCUGCAAAACCUACGUAGUCCCAUCUAUCAUGCUCGACCCUACGAGGCUAAUGUCUUGUCAGAGGCCCGUCAUGUGCCACGUACAUACACCAAUGUAUACCGCUCUAGCGGUUUGGUGUAGUAGGACUUGUGUAUGCACGCUACAGCGAACAACGUUGAUCCCUAACUGAAGUCGGGCUCCGCAGGCCUACUCACGCCGUUUCUAUAGGUUGAGCCGCAUCAAACAUUGGGUUGAGUCUCGAGUAUAGAGGAAGGCUCUGGUGGCAGGCGCGACGUUGAUCGGGAGGAGUAUGGAUGGUGAUCAAUCCCCGUGCCAAUCGCGAGUACUACAGGAGGAGGGGGCGGCUCUGUUCAAUCAUCACCCGUUCCAUCACACGGGCAGCACAGUUGACCUCCCGAGCCGUCUCACGGACCUAGUGGCAACAGGUGUAUUGAAGCGCCGGGAAUAGUCAUACCCGUGGGCUUGAUUGAGAGACCGAAAUUCCGACCGCCAAAACUGCUGAUAUCGUACGCCUUACUACAAAACAAAUGACGUCACUACCGGCCAGGGACAAGCUUAUUAAUUAAGUAGGAACCCUAUACCUUGCACAUCCUAAAUCUAGCAGCGGGUCCAGGAUUGGUUCCAGUCCAACGCGCGAUGCGCGUCAAGCUAGGCGAAUGACCACGGUCGAAACACCACUUAUGUGACCCACCUUGGCCAACUCUCCCGAUUCUCCUCGCUACUAUCUUGAAGGUCACUGAGAAUAUCCCUUAUGGGUCGCAUACGGAGACAGCCGCAGGAGCCUUAACGGAGAAUACGCCAAUACUAUGUUCUGGGUCGGUGGGUGUAAUGCGAUGCAAUCCGAUCGUGCGAACGUUCCCUUUGAUGACUAUAGGGUCUAGUGAUCGUACAUGUGC
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"""

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