Python for Biologists: A Complete Programming Course for Beginners

Description

Learning to program is one of the best investments that you can make for your research and your career. Python for biologists is a complete programming course for beginners that will give you the skills you need to tackle common biological and bioinformatics problems. Why learn programming? Maybe you see colleagues writing programs to save time and deal with large datasets. Maybe your supervisor has told you that you need to learn programming for your next project. Maybe you've been looking at job ads and noticed just how many of them are asking for programming skills. Table of contents In chapter one, you'll learn why Python is a good choice for biologists and beginners alike. You'll also learn how to install Python for your operating system and how to set up your programming environment, complete with links to all the free software you'll need. In chapter two, you'll learn how to manipulate text (including DNA and protein sequences) and how to fix errors in your programs. Exercises: calculating AT content, splicing introns. In chapter three, you'll learn how to read and write data to and from files. You'll also learn how to deal with file paths and the FASTA file format.Exercises: splitting genomic DNA, writing a FASTA file. In chapter four, you'll learn how to process many pieces of data in a single program and more advanced tools for sequence manipulation. Exercises: trimming adapter sequences, concatenating exons. In chapter five, you'll learn how to make Python even more useful by creating your own functions, including the best ways to test those functions in order to speed up development. Exercises: Analyzing the amino acid composition of protein sequences. In chapter six, you'll learn how to write programs that can make smart decisions about how to handle data and how to make your programs follow complex rules. Exercises: filtering genes based on multiple criteria. In chapter seven, you'll learn an incredibly powerful tool for working with patterns in text - regular expressions - and how to use it to search in DNA and protein sequences. Exercises: filtering accession names and calculating restriction fragment sizes. In chapter eight, you'll learn how to store huge amounts of data in a way that can still allows it to be retrived very efficiently. This allows simplification of much of the code from previous chapters. Exercises: translating DNA sequences to protein. In chapter nine, you'll learn how to make your Python programs work in harmony with existing tools, and how to polish up your programs so that they're ready for other people to use. Exercises: counting k-mers, binning DNA sequences by length. About the author Dr. Martin Jones has been teaching biologists to write software for over five years and has taught everyone from postgraduates to PIs. He is currently Lecturer in Bioinformatics at Edinburgh University. About the author Preface 1: Introduction and environment Why have a programming book for biologists? Why Python? Python vs. Perl How to use this book Exercises and solutions Getting in touch Setting up your environment Installing Python Running Python programs Python 2 vs. Python 3 Text editors Reading the documentation 2: Printing and manipulating text Why are we so interested in working with text? Printing a message to the screen Quotes are important Use comments to annotate your code Error messages and debugging Forgetting quotes Spelling mistakes Splitting a statement over two lines Printing special characters Storing strings in variables Tools for manipulating strings Concatenation Finding the length of a string Changing case Replacement Extracting part of a string Counting and finding substrings Splitting up a string into multiple bits Recap Exercises Calculating AT content Complementing DNA Restriction fragment lengths Splicing out introns, part one Splicing out introns, part two Splicing out introns, part three Solutions Calculating AT content Complementing DNA Restriction fragment lengths Splicing out introns, part one Splicing out introns, part two Splicing out introns, part three 3: Reading and writing files Why are we so interested in working with files? Reading text from a file Using open to read a file Files, contents and file names Dealing with newlines Missing files Writing text to files Opening files for writing Closing files Paths and folders Recap Exercises Splitting genomic DNA Writing a FASTA file Writing multiple FASTA files Solutions Splitting genomic DNA Writing a FASTA file Writing multiple FASTA files 4: Lists and loops Why do we need lists and loops? Creating lists and retrieving elements Working with list elements Writing a loop Indentation errors Using a string as a list Splitting a string to make a list Iterating over lines in a file Looping with ranges Recap Exercises Processing DNA in a file Multiple exons from genomic DNA Solutions Processing DNA in a file Multiple exons from genomic DNA 5: Writing our own functions Why do we want to write our own functions? Defining a function Calling and improving our function Encapsulation with functions Functions don't always have to take an argument Functions don't always have to return a value Functions can be called with named arguments Function arguments can have defaults Testing functions Recap Exercises Percentage of amino acid residues, part one Percentage of amino acid residues, part two Solutions Percentage of amino acid residues, part one Percentage of amino acid residues, part two 6: Conditional tests Programs need to make decisions Conditions, True and False if statements else statements elif statements while loops Building up complex conditions Writing true/false functions Recap Exercises Several species Length range AT content Complex condition High low medium Solutions Several species Length range AT content Complex condition High low medium 7: Regular expressions The importance of patterns in biology Modules in Python Raw strings Searching for a pattern in a string Alternation Character groups Quantifiers Positions Combining Extracting the part of the string that matched Getting the position of a match Splitting a string using a regular expression Finding multiple matches Recap Exercises Accession names Double digest Solutions Accession names Double digest 8: Dictionaries Storing paired data Creating a dictionary Iterating over a dictionary Iterating over keys Iterating over items Recap Exercises DNA translation Solutions DNA translation 9: Files, programs, and user input File contents and manipulation A note on the code examples Basic file manipulation Deleting files and folders Listing folder contents Running external programs Running a program Saving program output User input makes our programs more flexible Interactive user input Command line arguments Recap Exercises Binning DNA sequences Kmer counting Solutions Binning DNA sequences Kmer counting