辅导Homework 3 N.B.、讲解Python程序编程、辅导Python、辅导讲解Python设计

Homework 3

N.B.

Make sure your code is well documented with comments. Clearly mark different

sections of your code corresponding to the questions.

Any bonus point is not required, it is intended to supplement your python knowledge.

Remember to document your code! For example:

def myfunction(arg):

"""

This is a docstring. Surrounded by triple double-quotes. Description of

the whole function goes here. """

# This is a comment, provides concise description of following code.

pass

Your best resource for help is the official python documentation.

Questions

A. Sequence Tools

Write a Python module named seq_tools_netid.py that contains the following

functions:

1. load_fasta(filename)

Create a function named load_fasta that takes a filename (str) as input and

returns the sequence(s) (str) found in that file assuming it is a FASTA file

containing one or more sequences (using the FASTA file format).

2. get_reverse_complement(sequence)

Create a function named get_reverse complement that takes a sequence (str)

as input and returns the reverse of its complementary sequence (str). It is okay

to reuse a function from previous exercises.

3. get_transcript(sequence)

Create a function named get_transcript that takes a sequence (str) as input

and returns the RNA transcript produced from this sequence assuming the input

is the coding sense strand (Is this the same sequence as the RNA transcript

produced? You should know). It is okay to reuse a function from previous

exercises.

4. get_translation(sequence, reverse_complement_flag)

Create a function named get_translation that takes a sequence (str) as input

and returns the translated primary sequence produced from this sequence (i.e. a

protein sequence) assuming it represents a coding sequence. This function

should be able to properly translate a sequence representing DNA OR RNA. This

function should have a second argument (boolean) which defaults to False. If this

second argument is True, the function should return the translation of the reverse

complement of the input sequence. Use asterisk (*) for the stop codon.

5. Execution and test cases:

You should also include a function that shows some test cases for each function

e.g.Provide different sequences (some right, some wrong) to input into your

functions to test the output

o print(get_transcript('ATATDSTAV')) should give some error messages

o print(get_transcript('ATATTGTAC')) should give the correct output

B. Sequence Transcription and Translation

Write a Python script named transcribe_translate_netid.py which should import all

the functions from seq_tools_netid.py (both should be in the same directory). It should

take a filename as input, load sequence data from this file, and print the translation of

the sequence(s), each in a separate line.

If executed, this file should take 1 input argument (the filename to analyze). You should

use the functions imported from seq_tools_netid.py to perform these tasks.

Test Your Code

Test your script by running it on the following fasta files (attached with this homework)

and ensure that it runs without error and outputs only the translation of the

sequence(s). You can also include a check for empty fasta files (useful when fasta files

are empty).

Provided test files:

Single sequence in fasta file: one_nt_seq.fa

Multiple sequences in fasta file: multiple_nt_seq.fa

Submission

Submit the following python files to NYU classes:

1. seq_tools_netid.py

2. transcribe_translate_netid.py

3. Export your code and output as html file and submit the .html file with the results