Lecture 1

Course Details

• Course Title: BIOTECH4BI3 - BIOINFORMATICS
• Lecture 1: Python review and introduction to BioPython

Python Installation

• Use Anaconda: www.anaconda.com/products/individual
• Download Python 3.12 version suitable for your platform (Windows, Mac, Linux)
• Install the appropriate installer (different versions for Windows, Mac, and Linux). Windows has a 64-bit Graphical Installer (912.3M), Mac has a 64-bit (Apple silicon) Graphical Installer (704.7M), and Linux has a 64-bit (x86) Installer (1007.9M).

Python Fundamentals

• Extensive standard library
• Promotes easy addition of new functionality
• Code structure is crucial
• Proper use of English language keywords is essential (e.g., capitalization matters)
• "Clever" coding is not considered a positive attribute

Hello World! Example

• Each Python program typically starts with a declaration specifying the Python interpreter's location (often omitted on Windows)
• Use \n for newline characters
• Strings for text need quotation marks
• Save the program with a .py extension
• Execute the program using the python command

Data Types

• Python has built-in data types, including numbers (integers and floats) and strings
• Variables store data (e.g., myNumber = 1, mySentence = "You will love my class")
• Operators for data manipulation (e.g., +, -, *, /, %, **, <=, >=, !=, <, >).

Built-in Python Types

• Integers (int(x))
• Floats (float(x))
• Lists (e.g., myList=[1,2,3,'four'])
• Ranges (e.g., myRange=range(0,10,2))
• Strings (e.g., myString="biotech")
• Dictionaries (e.g., myHash={'Joe':123,'John':456})

Flow Control

• Python uses familiar constructs (e.g., if/elif/else, for statements, while statements, break, continue) for program flow control.

If/elif/else

• Conditional statements provide choices to actions
• If condition is true, execute operation 1
• If condition is false but elif condition is true , execute operation 2
• If neither condition is true, execute operation 3

For Loop Examples

• Used for looping through a defined or specified range
• Avoid infinite loops (ensure your loop counter changes value).
• Use indentation to structure your code within the loop

While Loop Examples

• Used for looping an indeterminate number of times
• The while loop continues executing as long as the logical value is True. Make a condition that changes from True to False to end the loop.

Lists

• List is a data structure for storing objects sequentially
• Create a list (e.g., myList = [])
• Add elements (myList.append(element))
• Add lists to lists (myList.extend(listToAppend))
• Insert elements (myList.insert(index, element))
• Delete elements (del myList[index], myList.pop(index))

Dictionaries

• A data structure for key-value pairs
• Create an empty dictionary (myBook = {})
• Add key-value pairs (myBook["one"] = 1)
• Delete key-value pairs (del myBook["one"], myBook.pop("one"))
• Accessing keys, values, and key-value pairs (myKeys=myBook.keys(), myValues=myBook.values(), for key, value in myBook.items())

Files

• Python has an easy way to access text files
• Use FILEHANDLE = open(FILE, mode='r') to open the file for reading
• FILEHANDLE = open(FILE, mode='w') to open to write, and FILEHANDLE = open(FILE, mode='a') for appending
• Reading a line from the file (myLine = myFile.readline())
• Writing to a file (myFile.write(“This is a text”))
• Closing the file (myFile.close())

Miscellaneous Commands

• str.rstrip() : Removes whitespace from the end of a string (by default). Can also remove newlines (\n) using str.rstrip('\n')
• ''.join(list): Joins the strings in a list into a single string.
• str.split() : Splits a string into a list of strings.
• str.find(): Finds the position of a substring within a string.
• str.replace(old,new) : Replaces occurrences of 'old' with 'new' in a string
• Replacing characters at specified positions (stringList[index]=newCharacter)

Error Handling

• A try...except block handles potential errors gracefully
• try block: Code that might raise an error.
• The except block: Handles the specific error type.
• finally block: Always executes regardless of errors, often for cleanup operations.

Command-line Arguments

• Pass information to a Python program at execution
• sys.argv stores the arguments
• programName = sys.argv[0] access file name
• arg1=sys.argv[1] access the first external argument input

Python Functions

• Reusable code blocks
• def FUNCTION_NAME(PARAMETERS): to define a function
• RETURN_VALUE to return data or execute an action

BioPython

• A collection of Python classes designed to handle bioinformatics tasks
• Facilitates processing BLAST reports and other bioinformatics data
• Useful for working with DNA sequences and converting between different formats (e.g., Genbank, FASTA, FASTQ

FASTA Format

• Standard format for DNA data exchange in bioinformatics.
• Each record starts with a ">" followed by a descriptive title.
• DNA data starts on the next line.

FASTQ Format

• Used for high-throughput DNA sequencing data.
• Contains base calls and quality scores.
• Each record has four lines:
  • The first line begins with an "@" symbol; provides identifying information.
  • The second line contains the DNA base sequence.
  • The third line begins with a "+" character.
  • The fourth line shows quality scores for corresponding bases.

Genbank Format

• Widely used format for nucleotide data in bioinformatics.
• Contains various metadata about the sequence including location, accession numbers, and references.

Bio.SeqIO

• A module in BioPython for parsing and writing sequence files in different formats.
• Often used for processing FASTA, GenBank, and other formats.

Bio.SearchIO

• Used to search a sequence against a database of sequences, specifically through programs like BLAST.
• Converts and processes results from BLAST reports.

Test your knowledge of Python programming and its applications in bioinformatics. This quiz covers essential Python concepts along with specific BioPython modules and file formats used in biological data analysis. Perfect for learners who want to assess their understanding of these two critical areas.