Python for Biologists

سرفصل های دوره

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

1. Requirements and tips for talking with a computer

1. Introduction

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

3. Ways to write and run python codes Interactive interpreter

4. Ways to write and run python codes Python script

5. Ways to write and run python codes IDE

6. Summary

7.1 C4.zip

7. Full course scripts.html

8. Create a variable

9. Create a variable.html

10. Tips for writing the variable name or identifier

11. Correct the code.html

12. Summary

13. Reduce the risk of using reserved words with the case sensitivity feature

14. Correct the code.html

15. Summary

16. The difference between comments and codes

17. Correct the code.html

18. Summary

19. Receiving and processing user data and producing output.

20. Correct the code.html

21. Summary

22. Optional tips for organizing variables

23. Summary

2. Data containers in python (types and conversions)

1. Refresh

2. Number data type

3. Create a variable that stores a number.html

4. String data type

5. Create a variable that stores a string.html

6. List and tuple data types

7. Create a variable that stores a list or tuple.html

8. Dictionary data type

9. Create a variable that stores a dictionary.html

10. Summary

11. The problem of receiving data, whether from the command interface or a file

12. Convert from an integer to a float or vice versa

13. Complete the code Convert from integer to float and vice versa.html

14. Work with the complex

15. Convert from a number to a string and vice versa

16. Complete the code Convert from a number to a string and vice versa.html

17. Complete the code Convert from a number to a string.html

18. Summary

19. Convert from a string to a list or tuple

20. Complete the code Convert from a string to a list or tuple.html

21. Convert from a list or tuple to a dictionary

22. Summary

3. Access the items in the data containers

1. Introduction

2. The forward index

3. The reverse index

4. Create a data type from items of another data type using the index

5. The dictionary key

6. Summary

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

1. Prepare and save external data in a data type in python Create small database

2. The first code Unraveling the mystery of the IUPAC ambiguity codes

3. The second code The inverse of the first code

5. Perform operations and set conditions or questions

1. Introduction Arithmetic operators Addition and subtraction

2. Arithmetic operators Multiplcation, division, floor division, and exponent

3. Arithmetic operators Modulus

4. Summary

5. Arithmetic operators Handling string and list

6. Summary

7. Arithmetic operators Operator precedence

8. Summary

9. Create a code that calculates extra nucleotides in DNA before translation

10. Create a code that calculates extra nucleotides in DNA before translation

11. Summary

12. Assignment operators

13. Summary

14. Comparison operators Equality

15. Comparison operators Greater than and less than

16. Summary

17. Create a code that compares two sequences in terms of both length and content

18. Summary

19. Membership operators

20. Summary

21. Create a code that searches for a restriction recognition site in DNA

22. Logical operators

23. Summary

24. Create a code that searches for MULTIPLE restriction recognition sites in DNA

25. Summary

26. Identity operators

27. Summary

28. Bitwise operators Convert from an integer to a binary and vice versa

29. Bitwise operators And, or, xor

30. Bitwise operators 2s complement, and left and right shift

31. Summary

6. Decision making support

1. If statement, if-else statement, and if-elif-else statement

2. Summary

3. Create a code that determines whether the sequence is DNA or RNA

4. Zero, non-zero, null, and non-null values

5. Nested if

7. Repeat commands in loops

1. The while loop

2. Summary

3. Calculating the GC content using the while loop

4. The for loop

5. Calculating the GC content using the for loop

6. Control loops with break, continue, and pass

7. Summary

8. Functions and methods for handling string data type

1. Review

2. Summary

3. Non-printable characters

4. Summary

5. String formatting part 1

6. Summary

7. String formatting part 2

8. Summary

9. Capitalize the first letter of a string

10. Center a string to total width columns

11. Left and right adjustment of a string for the total width of the columns

12. Count how many times a string or substring occurs in a string

13. Test if a string or substring of the string ends with a certain suffix

14. Test if a string or substring of the string starts with a certain prefix

15. Expand tabs in string to multiple spaces

16. Find starting index of a string or substring that occurs in a string

17. Find starting index of a string or substring that occurs backwards in a string

18. Search starting index of a string or substring that occurs in a string

19. Search starting index of a string or substring that occurs backwards in a string

20. Test if a string contains alphanumeric character(s)

21. Test if a string contains alphabetic character(s)

22. Test if a string contains digits only

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

24. The difference between numbers test

25. Test if a string contains white space(s)

26. Test if a string is a title and create title

27. Concatenate list or tuple items into a string

28. Obtain a string length

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

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

31. Replace a string or substring of a string part 1

32. Replace a string or substring of a string part 2

33. Create a translation table and translate a string

34. Obtain the minimum and maximum character from a string

35. Split a string based on delimiter string or substring to a list of substrings

36. Swap string characters from upper- to lowercase and vice versa

37. Fill a string using zero(s)

9. Functions and methods for handling list data type

1. Review

2. Obtain a list length, and minimum and maximum items of a list

3. Add an item to the end or certain location of a list

4. Extend a list by another list

5. Count how many times an item occurs in a list

6. Search starting index of an item that occurs in a string

7. Remove an item using its index or content

8. Sort list items

9. Reverse the order of a list

10. Remove a duplicate items of a list

10. Functions for handling tuple data type

1. Obtain a tuple length, and minimum and maximum items of a tuple

11. Functions and methods for handling dictionary data type

1. Review

2. Obtain a dictionary length

3. Remove dictionary items

4. Copy a dictionary

5. Convert a tuple items into a dictionary keys

6. Control errors while accessing the dictionary keys

7. Convert a dictionary to a list of tuples and extract keys and values separately

8. Update a dictionary

12. Handling files and operating systems

1. Review

2. Summary

3. The modes for opening a file.

4. Open a file for read-only purpose

5. Summary

6. Open a file for overwrite-only purpose

7. Convert fasta multi-lines to fasta two-lines Method1

8. Convert fasta multi-lines to fasta two-lines Method2

9. Open a file for append-only purpose

10. Summary

11. Open a file for read and write purposes

12. Summary

13. Open a file for write and read purposes

14. Summary

15. Open a file for append and read purposes

16. Summary

17. Dealing with the content of the open file for the purpose of reading

18. Dealing with read lines one by one

19. Output a list in a file

20. Read files with for loop Preserving memory from complexity

21. The second and preferred way to open files Don't be afraid to close files

22. Handle paths The current path and how to go and get the contents

23. Creating a folder or folders

24. Delete a folder

25. Delete folders

26. Rename a folder or folders

13. Handling time and date

1. Dealing with time and date

2. Which is faster Calculating the time taken for two GC content calculator codes

3. Dealing with a specific format of time and date in terms of output or reading

4. Wait in Python

14. Creating python function Arranging and organizing codes in an effective format

1. Modify some codes to use as examples

2. Modify some codes to use as examples

3. Create and call functions and the difference between print and return

4. Summary

5. The arguments and their function are pass-throughs of data across the function

6. Summary

7. Global (outside) variables and local (inside) variables

8. Summary

9. The required and default arguments and the argument keyword

10. Summary

11. Argument for unlimited items

12. Summary

13. The lambda as an alternative function in case of small code

14. Summary

15. Modules and scripts as a small product for your code

1. Import modules, see python paths, and import methods

2. Summary

3. Combine module and script using if name == main

4. Summary

5. Further clarification of the importance of if name == main

6. Summary

7. Further clarification of ways to import modules or functions within modules

8. Summary

9. Get global and local variables contained in functions

10. Summary

16. Create a python package from scratch Producing a python application for users

1. Obtain RNA-seq data from ENA Browser - European Nucleotide Archive.html

2. Create the first module to estimate the quality of nucleotides in the FASTQ file

3. Completing the creation of the first module

4. Summary

5. Improve the first module to deal with several files

6. Create the second module to convert a FASTQ file to a FASTA

7. Modifications to the second module

8. Create the third module to extract specific IDs from the FASTQ

9. Create the package First module test

10. Improving the first module to receive quality and its percentage from the user

11. Correction of errors discovered in the first module

12. The end A short story for the last tip

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تولید کننده: Udemy-Training