MBB110 Lecture 5: Regular Expressions & BioPython

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Questions and Answers

Which action correctly retrieves a list of all `.txt` files in a directory named `data` using the `glob` module?

`glob("data.txt")`
`glob("data/*")`
`glob("data/*.txt")` (correct)
`glob("*.txt/data")`

What is the purpose of the wildcard character `*` in a `glob` pattern?

Matches any single character in a filename.
Matches only a literal asterisk character in a filename.
Matches only files with extensions.
Matches zero or more occurrences of any character in a filename. (correct)

After obtaining a list of filenames with `glob`, what is the next recommended step for processing each file?

Using a loop to iterate through the list and apply a function to each file. (correct)
Converting the list to a string for easier manipulation.
Directly modifying the `file_list` variable in-place.
Deleting the list to free up memory.

Which code snippet correctly iterates through a list of files obtained via `glob` and applies a function called `process_file` to each?

<code>for file in file_list: process_file(file)</code> (D) Signup and view all the answers

Why is it beneficial to use existing parsers like BioPython when working with specific file formats like FASTA?

To simplify the code and reduce the likelihood of errors in parsing. (B) Signup and view all the answers

Given the regex `^A.*B$` and the strings 'ABC', 'aBC', 'AC', and 'CAB', which string(s) would be matched?

'ABC' and 'AC' (C) Signup and view all the answers

What does the following regular expression signify: `[^XYZ]`?

Matches any character that is not 'X', 'Y', or 'Z'. (D) Signup and view all the answers

Considering the Wordle-solving strategy, what information does a 'yellow' letter provide?

The letter is present in the word but not in the current position. (A) Signup and view all the answers

Based on the provided Wordle regex example, if the mystery word had 'T' in the first position, 'E' in the second position, and 'X' in the fifth position, which regex pattern would be most appropriate?

TE...X (C) Signup and view all the answers

Given the code snippet that loads words from a file and converts them to uppercase, why is the `.upper()` method used?

To facilitate case-insensitive matching during regex operations. (C) Signup and view all the answers

In BioPython, what is the primary purpose of the `SeqIO.parse()` function?

To parse a file format into SeqRecord objects for iteration. (A) Signup and view all the answers

Given a `SeqRecord` object named `sr` in BioPython, how would you correctly extract the sequence as a string, taking only the first 20 characters?

<code>str(sr.seq)[0:20]</code> (B) Signup and view all the answers

What is the expected output of the following code snippet, assuming `file_list` contains 11 FASTA files?

Each individual sequence from each FASTA file in <code>file_list</code>. (D) Signup and view all the answers

What is the purpose of the `glob` function in the provided code snippet?

To list all files matching a specified pattern. (C) Signup and view all the answers

Why is it important to check if a substring exists within a sequence string before attempting to use it?

To avoid errors that may occur if the substring is not found. (C) Signup and view all the answers

In the context of sequence analysis, searching for patterns in biological sequences is crucial for which of the following reasons?

Discovering functional elements and motifs. (A) Signup and view all the answers

Assume you have a FASTA file containing multiple gene sequences. You want to extract the sequence IDs and the first 50 bases of each sequence. Which of the following code snippets correctly accomplishes this?

<code>for record in SeqIO.parse(fasta_file, "fasta"): print(record.id, str(record.seq)[:50])</code> (C) Signup and view all the answers

Given the following code snippet, what will be the output?

mwah mwah mwahhhhh (A) Signup and view all the answers

When using regular expressions, what is the primary function of defining a character class within square brackets `[]`?

To match any single character from the set of characters defined within the brackets. (A) Signup and view all the answers

In the context of regular expressions, what is the difference between using `*` and `+` as meta-characters?

<code>*</code> matches zero or more occurrences, while <code>+</code> matches one or more occurrences. (A) Signup and view all the answers

If you want to find all instances of the letter 'G' appearing exactly four times in a row, which regular expression pattern should you use?

G{4} (A) Signup and view all the answers

Which of the following regular expressions is correctly structured to identify valid Canadian postal codes, as described?

[A-Z][0-9][A-Z]\s[0-9][A-Z][0-9] (C) Signup and view all the answers

What is the purpose of the `re.compile()` function in Python's `re` module?

To pre-compile a regular expression pattern for more efficient matching. (D) Signup and view all the answers

If you have a list of DNA sequences and want to identify sequences that start with 'ATG' and end with 'TAA', which regular expression would be most appropriate?

^ATG.*TAA$ (B) Signup and view all the answers

Which of the following is NOT a typical application of regular expressions in bioinformatics?

Simulating protein folding dynamics. (C) Signup and view all the answers

Given the python code: `pattern = re.compile("[A-Z][0-9][A-Z]\s[0-9][A-Z][0-9]")` and the string `B2C 5X9`, what will be the output of `pattern.match("B2C 5X9")`?

Null (D) Signup and view all the answers

Which of the following statements accurately describes a Python dictionary?

Its elements are unordered, and it is mutable. (B) Signup and view all the answers

Using the provided genetic code dictionary, what amino acid does the codon 'GCA' code for?

A (A) Signup and view all the answers

If `maybe_cds` is 'AUGAAC', what would be the output of `genetic_code[maybe_cds[3:6]]`?

N (D) Signup and view all the answers

In the mRNA translation example, what is the purpose of the `break` statement within the loop?

To halt the translation process upon encountering a stop codon. (B) Signup and view all the answers

Given the genetic code and the sequence `maybe_cds = 'ATGCGATTTA'`, what will be the value of `num_aa` after the provided code is executed?

3 (A) Signup and view all the answers

Which of the following is NOT a characteristic of genomic sequence data that aids in predicting genes and gene products?

Amino acid charge. (C) Signup and view all the answers

If `cdna = 'ATTATGAACTGGCACATG'`, what is the purpose of the `cdna[11:]` operation in the provided code?

To remove the first 11 characters of the <code>cdna</code> sequence. (D) Signup and view all the answers

If the loop iterated through the entire `maybe_cds` string without encountering a stop codon, what would be the final value of the `peptide` variable?

A string containing all amino acids coded for by <code>maybe_cds</code>. This does not include stop codons. (B) Signup and view all the answers

What is the purpose of using `[^XYZ]` within a regular expression?

To match any character that is NOT X, Y, or Z. (C) Signup and view all the answers

In the Wordle example, the regex `pattern1 = re.compile("[^S][^N][^A][^K]E")` is used after guessing 'SNAKE'. What is the primary purpose of this pattern?

To find words that end in 'E' and do not have S, N, A, or K in the first four positions. (C) Signup and view all the answers

Which regular expression pattern will exclusively match the string 'RUN' and no other strings like 'RUNS' or 'MARUN'?

<code>^RUN$</code> (C) Signup and view all the answers

What is the main objective of the 'mRNAdle' task described in the text?

To locate the protein-coding sequence (CDS) within a cDNA sequence and predict the corresponding protein. (D) Signup and view all the answers

In the 'mRNAdle' approach, why is it important to search for start codons on both strands of the cDNA sequence?

To identify potential protein-coding regions regardless of which strand the gene is encoded on. (A) Signup and view all the answers

Within the 'mRNAdle' methodology, the lengths of translated protein sequences are compared. What is the underlying assumption that makes this comparison a useful step in identifying the correct CDS?

The longest open reading frame (ORF) within a given region is often the functional protein-coding sequence. (C) Signup and view all the answers

To find 5-letter words where the first letter is not 'X', 'Y', or 'Z', and the second letter is not 'P' or 'Q', which regular expression pattern is most appropriate?

<code>[^XYZ][^PQ]...</code> (A) Signup and view all the answers

Consider the Wordle regex `[^S][^N][^A][^K]E` from the guess 'SNAKE'. If the pattern was mistakenly changed to `[^S][^N][A][^K]E`, what would be the consequence of this modification?

The pattern would now match words where the third letter must be 'A', and the other positional exclusions remain the same. (A) Signup and view all the answers

Flashcards

Glob Package

A package in Python that finds pathnames matching a specified pattern.

Wildcard (*)

A character that matches any string of characters in filename patterns.