Python For Biologists

Bioinformatics, computational biology, biotechnology, genetics, molecular biology, microbiology, etc. need Python

What you'll learn

The Python syntax

The data types and conversions

Performing operations and setting different conditions or questions

Making decisions and using loops

The functions and methods that deal with data types

Opening, creating, reading and writing files

Working with the operating system

Handling time and date

Creating your own functions

Creating your own modules and scripts

Creating your own packages

Requirements

The latest version of Python is required to be installed. (Explained inside the course)

Visual studio code is required to be installed. (Explained inside the course)

The Microsoft Python extension for visual studio code is required to be installed. (Explained inside the course)

Description

Course descriptionThis course is designed for beginners in programming with a biological background who want to deal with biotechnology data such as DNA, RNA, and protein, or who want to enter the field of bioinformatics.This course requires you to install Python (this was explained in detail in the first section), and we will also need to install the Integrated Development Environment in order to write codes in it (this was also explained in the first section).All the Python files in which the codes were written, which you will see in the videos from the beginning to the end of the course, we have provided in a folder that you will download from the first section of the course.I want you to read this well because it will explain many things to you that will help you to continue learning the Python language by clarifying the fruit of each section of the course.In the first section, you will install Python, then you will know the modes through which you can write the codes, then you will learn the basics of the Python language, such as variables and what is related to them, comments, printing data to the user, and receiving data from the user.From this part, you will be able to learn how to receive data from the user, how to store the data inside the code, and how to output data to the user.In the second section, you will learn about data types in Python. The meaning of data types in Python is the form in which Python understands user data. And you will learn about converting from one data type to another.One of the fruits of the first section is storing data in variables. Here you will learn more about the format in which the data will be stored in these variables, and this varies according to the nature of the data that the user will enter. It may be a number, DNA sequence, table, file, and so on.In the third section, you will learn how to access just one element of data.After storing the data in a type of Python data, you will be able to delve into the data through Python, so you can access a very small part of the data and thus be able to deal with it however you want.In the fourth section, you will work with me on simple code. We will rely mostly on the information that we learned in the first three sections, where we will store data in Python, then receive data from the user, then search for it in the stored data, and output information to the user related to the information entered.In the fifth section, which is extremely important, we will learn operations that can be performed on the entered data and how the data can be updated. We will also put questions or conditions about the data that will give us one of two answers, either true or false.This section will give you the power to make decisions about the data.In the sixth section, you will learn how to write your decisions in code and help write procedures based on the decisions made.This part is very related to the fifth part, so they must be linked together.In the seventh section, you will learn how to use loops.These are precisely the ones that a person is unable to perform because they are characterized by repeating a set of commands at the speed of a computer, and therefore they can do complex things that a person cannot do in a short time, and therefore you must understand them well.In the eighth, ninth, tenth, and eleventh sections, we will learn many functions in Python that manipulate data.Knowing many functions enables the programmer to manipulate data, which is reflected in the effectiveness of the extracted information.In the twelfth section, one of the most important sections in the language in general and in the field of bioinformatics in particular, in which you will learn a new method of input and output, where input and output were functions, but now they are files, which are the biological data storage unit.You will also handle operating system paths within Python.In the thirteenth section, you will learn how to deal with time and date, and this section may be useful in calculating the time and printing it in the output.You will find, for example, in some programs that contain more than one process, that the time and date are printed for each process.In the fourteenth section, you will learn how to separate code and put it into structures that only work by calling, which is building your own functions.This is the first way to build the code for the user in a usable form.In the fifteenth section, you will learn to build scripts and modules that are considered the official output from the codes. That is, once you reach this stage, you can create your codes in modules that can be imported into Python easily.In the sixteenth section, you will learn to build the package, which is a collection of modules.There will be a project consisting of three modules that will be implemented step by step in front of you, and there will be improvements and error corrections, and therefore you will get good information and experience from this section.In the end, you will find that the course will teach you information and experiences about how to receive data from the user, how to deal with it, and finally how to output the information that the user wants.This is what you will need to build your code, whether it will be complete applications or some code that deals with data slightly, or contribute to the use of existing Python packages.

Overview

Section 1: Requirements and tips for talking with a computer

Lecture 1 Introduction

Lecture 2 Defining the programming language and installing python on Windows and Mac

Lecture 3 Ways to write and run python codes | Interactive interpreter

Lecture 4 Ways to write and run python codes | Python script

Lecture 5 Ways to write and run python codes | IDE

Lecture 6 Summary

Lecture 7 Full course scripts

Lecture 8 Create a variable

Lecture 9 Tips for writing the variable name or identifier

Lecture 10 Summary

Lecture 11 Reduce the risk of using reserved words with the case sensitivity feature

Lecture 12 Summary

Lecture 13 The difference between comments and codes

Lecture 14 Summary

Lecture 15 Receiving and processing user data and producing output.

Lecture 16 Summary

Lecture 17 Optional tips for organizing variables

Lecture 18 Summary

Section 2: Data containers in python (types and conversions)

Lecture 19 Refresh

Lecture 20 Number data type

Lecture 21 String data type

Lecture 22 List and tuple data types

Lecture 23 Dictionary data type

Lecture 24 Summary

Lecture 25 The problem of receiving data, whether from the command interface or a file

Lecture 26 Convert from an integer to a float or vice versa

Lecture 27 Work with the complex

Lecture 28 Convert from a number to a string and vice versa

Lecture 29 Summary

Lecture 30 Convert from a string to a list or tuple

Lecture 31 Convert from a list or tuple to a dictionary

Lecture 32 Summary

Section 3: Access the items in the data containers

Lecture 33 Introduction

Lecture 34 The forward index

Lecture 35 The reverse index

Lecture 36 Create a data type from items of another data type using the index

Lecture 37 The dictionary key

Lecture 38 Summary

Section 4: Congratulations, this is your first program using the Python language

Lecture 39 Prepare and save external data in a data type in python | Create small database

Lecture 40 The first code | Unraveling the mystery of the IUPAC ambiguity codes

Lecture 41 The second code | The inverse of the first code

Section 5: Perform operations and set conditions or questions

Lecture 42 Introduction | Arithmetic operators | Addition and subtraction

Lecture 43 Arithmetic operators | Multiplcation, division, floor division, and exponent

Lecture 44 Arithmetic operators | Modulus

Lecture 45 Summary

Lecture 46 Arithmetic operators | Handling string and list

Lecture 47 Summary

Lecture 48 Arithmetic operators | Operator precedence

Lecture 49 Summary

Lecture 50 Create a code that calculates extra nucleotides in DNA before translation

Lecture 51 Create a code that calculates extra nucleotides in DNA before translation

Lecture 52 Summary

Lecture 53 Assignment operators

Lecture 54 Summary

Lecture 55 Comparison operators | Equality

Lecture 56 Comparison operators | Greater than and less than

Lecture 57 Summary

Lecture 58 Create a code that compares two sequences in terms of both length and content

Lecture 59 Summary

Lecture 60 Membership operators

Lecture 61 Summary

Lecture 62 Create a code that searches for a restriction recognition site in DNA

Lecture 63 Logical operators

Lecture 64 Summary

Lecture 65 Create a code that searches for MULTIPLE restriction recognition sites in DNA

Lecture 66 Summary

Lecture 67 Identity operators

Lecture 68 Summary

Lecture 69 Bitwise operators | Convert from an integer to a binary and vice versa

Lecture 70 Bitwise operators | And, or, xor

Lecture 71 Bitwise operators | 2s complement, and left and right shift

Lecture 72 Summary

Section 6: Decision making support

Lecture 73 If statement, if-else statement, and if-elif-else statement

Lecture 74 Summary

Lecture 75 Create a code that determines whether the sequence is DNA or RNA

Lecture 76 Zero, non-zero, null, and non-null values

Lecture 77 Nested if

Section 7: Repeat commands in loops

Lecture 78 The while loop

Lecture 79 Summary

Lecture 80 Calculating the GC content using the while loop

Lecture 81 The for loop

Lecture 82 Calculating the GC content using the for loop

Lecture 83 Control loops with break, continue, and pass

Lecture 84 Summary

Section 8: Functions and methods for handling string data type

Lecture 85 Review

Lecture 86 Summary

Lecture 87 Non-printable characters

Lecture 88 Summary

Lecture 89 String formatting part 1

Lecture 90 Summary

Lecture 91 String formatting part 2

Lecture 92 Summary

Lecture 93 Capitalize the first letter of a string

Lecture 94 Center a string to total width columns

Lecture 95 Left and right adjustment of a string for the total width of the columns

Lecture 96 Count how many times a string or substring occurs in a string

Lecture 97 Test if a string or substring of the string ends with a certain suffix

Lecture 98 Test if a string or substring of the string starts with a certain prefix

Lecture 99 Expand tabs in string to multiple spaces

Lecture 100 Find starting index of a string or substring that occurs in a string

Lecture 101 Find starting index of a string or substring that occurs backwards in a string

Lecture 102 Search starting index of a string or substring that occurs in a string

Lecture 103 Search starting index of a string or substring that occurs backwards in a string

Lecture 104 Test if a string contains alphanumeric character(s)

Lecture 105 Test if a string contains alphabetic character(s)

Lecture 106 Test if a string contains digits only

Lecture 107 Test if a string contains upper- or lower-case and convert from one to another

Lecture 108 The difference between numbers test

Lecture 109 Test if a string contains white space(s)

Lecture 110 Test if a string is a title and create title

Lecture 111 Concatenate list or tuple items into a string

Lecture 112 Obtain a string length

Lecture 113 Remove leading or tailing character(s) or from both sites of a string part 1

Lecture 114 Remove leading or tailing character(s) or from both sites of a string part 2

Lecture 115 Replace a string or substring of a string part 1

Lecture 116 Replace a string or substring of a string part 2

Lecture 117 Create a translation table and translate a string

Lecture 118 Obtain the minimum and maximum character from a string

Lecture 119 Split a string based on delimiter string or substring to a list of substrings

Lecture 120 Swap string characters from upper- to lowercase and vice versa

Lecture 121 Fill a string using zero(s)

Section 9: Functions and methods for handling list data type

Lecture 122 Review

Lecture 123 Obtain a list length, and minimum and maximum items of a list

Lecture 124 Add an item to the end or certain location of a list

Lecture 125 Extend a list by another list

Lecture 126 Count how many times an item occurs in a list

Lecture 127 Search starting index of an item that occurs in a string

Lecture 128 Remove an item using its index or content

Lecture 129 Sort list items

Lecture 130 Reverse the order of a list

Lecture 131 Remove a duplicate items of a list

Section 10: Functions for handling tuple data type

Lecture 132 Obtain a tuple length, and minimum and maximum items of a tuple

Section 11: Functions and methods for handling dictionary data type

Lecture 133 Review

Lecture 134 Obtain a dictionary length

Lecture 135 Remove dictionary items

Lecture 136 Copy a dictionary

Lecture 137 Convert a tuple items into a dictionary keys

Lecture 138 Control errors while accessing the dictionary keys

Lecture 139 Convert a dictionary to a list of tuples and extract keys and values separately

Lecture 140 Update a dictionary

Section 12: Handling files and operating systems

Lecture 141 Review

Lecture 142 Summary

Lecture 143 The modes for opening a file.

Lecture 144 Open a file for read-only purpose

Lecture 145 Summary

Lecture 146 Open a file for overwrite-only purpose

Lecture 147 Convert fasta multi-lines to fasta two-lines | Method1

Lecture 148 Convert fasta multi-lines to fasta two-lines | Method2

Lecture 149 Open a file for append-only purpose

Lecture 150 Summary

Lecture 151 Open a file for read and write purposes

Lecture 152 Summary

Lecture 153 Open a file for write and read purposes

Lecture 154 Summary

Lecture 155 Open a file for append and read purposes

Lecture 156 Summary

Lecture 157 Dealing with the content of the open file for the purpose of reading

Lecture 158 Dealing with read lines one by one

Lecture 159 Output a list in a file

Lecture 160 Read files with for loop | Preserving memory from complexity

Lecture 161 The second and preferred way to open files | Don't be afraid to close files

Lecture 162 Handle paths | The current path and how to go and get the contents

Lecture 163 Creating a folder or folders

Lecture 164 Delete a folder

Lecture 165 Delete folders

Lecture 166 Rename a folder or folders

Section 13: Handling time and date

Lecture 167 Dealing with time and date

Lecture 168 Which is faster?| Calculating the time taken for two GC content calculator codes

Lecture 169 Dealing with a specific format of time and date in terms of output or reading

Lecture 170 Wait in Python

Section 14: Creating python function | Arranging and organizing codes in an effective format

Lecture 171 Modify some codes to use as examples

Lecture 172 Modify some codes to use as examples

Lecture 173 Create and call functions and the difference between print and return

Lecture 174 Summary

Lecture 175 The arguments and their function are pass-throughs of data across the function

Lecture 176 Summary

Lecture 177 Global (outside) variables and local (inside) variables

Lecture 178 Summary

Lecture 179 The required and default arguments and the argument keyword

Lecture 180 Summary

Lecture 181 Argument for unlimited items

Lecture 182 Summary

Lecture 183 The lambda as an alternative function in case of small code

Lecture 184 Summary

Section 15: Modules and scripts as a small product for your code

Lecture 185 Import modules, see python paths, and import methods

Lecture 186 Summary

Lecture 187 Combine module and script using if name == main

Lecture 188 Summary

Lecture 189 Further clarification of the importance of if name == main

Lecture 190 Summary

Lecture 191 Further clarification of ways to import modules or functions within modules

Lecture 192 Summary

Lecture 193 Get global and local variables contained in functions

Lecture 194 Summary

Section 16: Create a python package from scratch | Producing a python application for users

Lecture 195 Obtain RNA-seq data from ENA Browser - European Nucleotide Archive

Lecture 196 Create the first module to estimate the quality of nucleotides in the FASTQ file

Lecture 197 Completing the creation of the first module

Lecture 198 Summary

Lecture 199 Improve the first module to deal with several files

Lecture 200 Create the second module to convert a FASTQ file to a FASTA

Lecture 201 Modifications to the second module

Lecture 202 Create the third module to extract specific IDs from the FASTQ

Lecture 203 Create the package | First module test

Lecture 204 Improving the first module to receive quality and its percentage from the user

Lecture 205 Correction of errors discovered in the first module

Lecture 206 The end | A short story for the last tip

Biologists working with biotechnology data in any discipline.,Beginners in programming.,Beginners in Python.