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Python end of life or By default, the end-of-life is scheduled 5 years after the first release, but can be adjusted by the release manager of each branch.

Install, setup

Multiple python versions

How to use pyenv to run multiple versions of Python on a Mac


# check pip version
python -m pip --version

# install
curl -o

# Upgrading pip
python -m pip install -U pip
  • On my 2018 mac, the default python3 is at "/usr/local/bin/pyhton3". In "~/Library/Python" directory, it has "2.7", "3.8" and "3.9".
  • On my 2021 mac Ventura, the default python3 is at "/usr/bin". But when we try to run 'python3', it asked to install the command line developer tools. After the installation we can use python3. Still, there is no "~/Library/Python" directory.

Online compiler


  • PyCharm
  • Thonny
  • Spyder
  • RStudio
    • Create a file (
    • Click the terminal tab. Type 'python' (or ipython3).
    • Use Ctrl/CMD + Alt + Enter to run your python code line by line or a chunk.

Visual Studio Code

The ipynb file can contain figures.

This (Harmony Manuscript) has several notebook files where the code in ipynb files were written in R, not Python.

I can use vsc to open a ipynb file.




Emacs Shell mode: how to send region to shell?


  • What is the difference between Jupyter Notebook and JupyterLab?
  • Jupyter Notebook (classic) and JupyterLab are both web-based interactive computing environments for working with data and code, but they have some key differences in terms of their user interface, features, and capabilities.
  • JupyterLab is a more modern and powerful tool than Jupyter Notebook, and is recommended for users who want a more flexible and feature-rich interface for working with data and code. However, Jupyter Notebook remains a popular and widely used tool, particularly for working with Jupyter notebooks.
  • 7 Reasons Why You Should Use Jupyterlab for Data Science

Some resources

Different installation methods

JupyterLab Desktop

pip/pip3 Jupyter

    which python3
    # /usr/bin/python3
    pip3 install jupyterlab
    # http://localhost:8888/lab
    # The current directory will be available on the file browser panel in JupyterLab.

    On Mac, it shows the following when I run 'pip3 install jupyterlab'

    Installing collected packages: pip
      WARNING: The scripts pip, pip3 and pip3.9 are installed in '/Users/XXX/Library/Python/3.9/bin' which is not on PATH.
      Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
    Successfully installed pip-23.0
    WARNING: You are using pip version 21.2.4; however, version 23.0 is available.
    You should consider upgrading via the '/Library/Developer/CommandLineTools/usr/bin/python3 -m pip install --upgrade pip' command.

    That is, I need to use /Users/XXX/Library/Python/3.9/bin/jupyter-lab to launch jupyter-lab OR add the path to ".zshrc"; see jupyterlab doc.

conda + Jupyter

conda install --yes jupyterlab && conda clean --yes --all

IPython shell

Extract python code from Jupyter notebook

Google colab

R programming

Setup Jupyter Notebook for R or Using R on Jupyter Notebook

To use R in JupyterLab, you will first need to install the IRkernel package in your R environment using the following command:


Once you have installed the IRkernel package, you can register it with JupyterLab using the following command in your R console:


After you have registered the kernel, you can start a new Jupyter notebook or JupyterLab session and select the "R" kernel from the kernel dropdown menu. This will allow you to run R code in JupyterLab, including data analysis, visualization, and other tasks.

Run Jupyter Notebooks on an Apple M1 Mac

Cheat sheet

The Most Frequently Asked Questions About Python Programming



Use Ctrl+d to quit.

How to run a python script file


Run python statements from a command line

Use -c (command) option.

python -c "import psutil"

run python source code line by line

run python source code line by line

python -m pdb <>

Install a new module

  • See an example of installing HTSeq.

Module != Package

  • A Python module is a single file containing Python code, while a package is a collection of modules organized in a specific way.
  • A module has a filename with the suffix .py added.

PyPI/Python Package Index


pip, use PyPI as the default source for packages and their dependencies.

As an example, motionEye can be installed by pip install or pip2 install; see its wiki and source code on Github.

sudo apt-get install python-pip
pip --version
pip install SomePackage
pip show --files SomePackage
pip install --upgrade SomePackage
pip install --upgrade 
pip install ‐‐upgrade pip  # Upgrade itself
pip uninstall SomePackage

sudo apt install python3-pip
pip3 --version

Upgrade packages

How to Upgrade Python Packages with Pip

List installed packages and their versions, location/directory

pip3 list -v

On my Ubuntu 20.04, the packages installed by pip3 is located in ~/.local/lib/python3.8/site-packages/. It does not matter where I issued the pip3 install command.

The danger of upgrading pip

Don't use sudo + pip

"--user" option in pip

$ pip install Pygments
OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/Pygments-2.2.0.dist-info'
/usr/local/lib/python2.7/dist-packages/pip-9.0.1-py2.7.egg/pip/_vendor/requests/packages/urllib3/util/ InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see
$ pip install --user Pygments
Collecting Pygments
  Using cached Pygments-2.2.0-py2.py3-none-any.whl
Installing collected packages: Pygments
Successfully installed Pygments-2.2.0

pip -t option

We can force to install a package in user's directory (i.e. a package is already installed in the global directory /usr/lib/python3/dist-packages but some applications cannot find it). Pip install python package into a specific directory other than the default install location

pip3 install -t ~/.local/bin/python3.10/site-packages pytz


Python “Virtual Environments” allows us to install a Python package in an isolated location, rather than installing it globally.

  • How To Manage Python Packages Using Pip. First Create a new project folder and cd to the project folder in your terminal.
    # Python 2
    $ sudo pip install virtualenv
    $ virtualenv <DIR_NAME>
    $ source <DIR_NAME>/bin/activate
    (<DIR_NAME>) ~$ which python
    $ deactivate
    # Python 3,
    $ python3 -m venv <DIR_NAME>  # DIR_NAME is also called an environment
    $ source <DIR_NAME>/bin/activate
    (<DIR_NAME>) ~$ which python
    $ deactivate

    Here is an example

    ~/github/PUREE$ python3 -m venv myenv
    The virtual environment was not created successfully because ensurepip is not
    available.  On Debian/Ubuntu systems, you need to install the python3-venv
    package using the following command.
        apt install python3.10-venv
    ~/github/PUREE$ sudo apt install python3.10-venv
    ~/github/PUREE$ python3 -m venv myenv
    ~/github/PUREE$ source myenv/bin/activate
    (myenv) ~/github/PUREE$ which python
    (myenv) ~/github/PUREE$ pip freeze > requirements.txt
    (myenv) ~/github/PUREE$ deactivate
    ~/github/PUREE$ ls myenv/bin
    activate  f2py   f2py3.10    pip   pip3.10  python3     wheel
    activate.csh  Activate.ps1   f2py3  normalizer  pip3  python   python3.10
  • Python Tutorial: virtualenv and why you should use virtual environments. pip freeze.
    pip list
    pip freeze --local > requirements.txt
    pip install -r requirements.txt
    pip list


  • Why Use Pipenv to Create a Python Environment?
  • Pipenv is a Python virtualenv management tool that supports a multitude of systems and nicely bridges the gaps between pip, pyenv and virtualenv. It automatically creates and manages a virtualenv for your projects, as well as adds/removes packages from your Pipfile as you install/uninstall packages. It also generates the ever-important Pipfile.lock, which is used to produce deterministic builds.


  • Poetry is a tool for dependency management and packaging in Python. It allows you to declare the libraries your project depends on and it will manage (install/update) them for you. Poetry offers a poetry.lock lockfile to ensure repeatable installs, and can build your project for distribution.

pipx (alternative to pip3)

  • Pipx is a tool that helps you install and run end-user applications written in Python. It is similar to macOS’s brew, JavaScript’s npx, and Linux’s apt.
    • Pipx is focused on installing and managing Python packages that can be run from the command line directly as applications.
    • pipx is made specifically for application installation, as it adds isolation yet still makes the apps available in your shell: pipx creates an isolated environment for each application and its associated packages.
    python3 -m pip install --user pipx
    python3 -m pipx ensurepath
    # OR sudo apt install pipx   
    # Or pip3 install pipx
    pipx install <package_name> # no sudo needed
    pipx list
    pipx uninstall <package_name>
  • I need to find an alternative to pip utility because of a problem when I used pip command. Error: externally-managed-environment
  • Official website [1] - Install and Run Python Applications in Isolated Environments, github
  • pipx vs pip
    • pipx is made specifically for application installation and adds isolation yet still makes the apps available in your shell. pipx creates an isolated environment for each application and its associated packages. On the other hand, pip is a general-purpose package installer for both libraries and apps with no environment isolation.
    • If you want to install an application that has dependencies that conflict with other applications or libraries on your system, you can use pipx to create an isolated environment for that application and its dependencies. This way, you can avoid conflicts between different versions of the same package.
    • On my Ubuntu, pip installs packages to /usr/local/lib/python3.8/dist-packages/.
  • Pipx – Install And Run Python Applications In Isolated Environments
  • Run Python applications in virtual environments


If a package has been bundled by its creator using the standard approach to bundling modules (with Python’s distutils tool), all you need to do is download the package, uncompress it and type:

python build
sudo python install

For Python 2, the packages are installed under /usr/local/lib/python2.7/dist-packages/.

$ ls -l /usr/local/lib/python2.7/dist-packages/
total 12
-rw-r--r-- 1 root staff  273 Jan 12 13:45 easy-install.pth
drwxr-sr-x 4 root staff 4096 Jan 12 13:45 HTSeq-0.6.1p1-py2.7-linux-x86_64.egg
drwxr-sr-x 4 root staff 4096 Jan 12 13:42 pysam-

python bdist_wheel

Get a list of installed modules

pydoc modules

Not helpful. See the pip list command.

Check installed packages' versions

If you install packages through pip, use

$ pip list
pyOpenSSL (0.13.1)
pyparsing (2.0.1)
pysam (0.10.0)
python-dateutil (1.5)
pytz (2013.7)
rudix (2016.12.13)
scipy (0.13.0b1)
setuptools (1.1.6)
singledispatch (
six (1.4.1)
tornado (4.4.2)
vboxapi (1.0)
xattr (0.6.4)
zope.interface (4.1.1)

And more information about a package by using pip show PACKAGE.

$ pip show pysam
Name: pysam
Version: 0.10.0
Summary: pysam
Author: Andreas Heger
Author-email: [email protected]
License: MIT
Location: /Users/XXX/Library/Python/2.7/lib/python/site-packages

The following method works whether the package is installed by source or binary package

>>> import pysam
>>> print(pysam.__version__)
>>> print pysam.__version__


Install a specific version of package through pip

For example, pysam package was actively released. But the new release ( may introduce some bugs. So I have to install an older version (0.10.0 works for me on Mac El Capitan and Sierra).

$ sudo -H pip uninstall pysam
Uninstalling pysam-
$ sudo -H pip install pysam==0.10.0
Collecting pysam==0.10.0
  Downloading pysam-0.10.0.tar.gz (2.3MB)
    100% |████████████████████████████████| 2.3MB 418kB/s 
Installing collected packages: pysam
  Running install for pysam ... done
Successfully installed pysam-0.10.0

warning: Please check the permissions and owner of that directory

I got this message when I use root to run the 'sudo pip install PACKAGE' command.


python3-pip installed but pip3 command not found?

sudo apt-get remove python3-pip; sudo apt-get install python3-pip

DeepSurv example

git clone
sudo cp /usr/bin/pip /usr/bin/pip.bak
sudo nano /usr/bin/pip # See more detail

# Method 1 for Theano
sudo pip install theano
# Method 2 for Theano
pip install --user --upgrade 

pip install --user --upgrade
cd DeepSurv/
pip install . --user
sudo apt install python-pytest
pip install h5py --user
sudo pip uninstall protobuf #
pip install protobuf --user
sudo apt install python-tk
============ test session starts ===========
platform linux2 -- Python 2.7.12, pytest-2.8.7, py-1.4.31, pluggy-0.3.1
rootdir: /home/brb/github/DeepSurv, inifile:
collected 7 items

tests/ .......

========== 7 passed in 5.77 seconds ========

How to list all installed modules

help('modules')  # the output is not pretty


  1. Use the comment symbol # for a single line
  2. Use a delimiter “”” on each end of the comment. Attention: Don't use triple-quotes

Python Comments from


Try / Except

Try and Except in Python

    number = int(input("Enter a number: "))
    print("Invalid Input")

if __name__ == "__main__":

How to Get the Current Directory in Python

How to Get the Current Directory in Python

Import a compiled C module

string and string operators


  1. Python for Genomic Data Science from coursera.
  2. Python Hello World and String Manipulation
dna[-1]='c' (start counting from the right)
dna[0:3]='gat' (the end always excluded)
dna.find('ag')=3  (only the first occurrence of 'ag' is reported)
dna.find('17', 2) (start looking from pos 17)
dna.rfind('ag')   ( search backwards in string)
dna.islower()    (True)
dna.isupper()    (False)
dna.replace('a', 'A')


Format Specification Mini-Language

Regular expression

The Beginner’s Guide to Regular Expressions With Python

User's input

dna=raw_input("Enter a DNA sequence: ")  # python 2
dna=input("Enter a DNA sequence: ")      # python 3

To convert a user's input (a string) to others

int(x, [, base])
str(x) #converts x to a string
str(65) # '65'

chr(x)  # converts an integer to a character
chr(65) # 'A'


Why is parenthesis in print voluntary in Python 2.7?

Fancy Output

print("THE DNA's GC content is ", gc, "%") # gives too many digits following the dot
print("THE DNA's GC content is %5.3f %%" % " % gc) 
# the percent operator separating the formatting string and the value to
# replace the format placeholder
print("%d" % 10.6)  # 10
print("%e" % 10.6)  # 10.060000e+01
print("%s" % dna)   # gatagc


Built-in Functions, How to check type of variable (object) in Python



A list is an ordered set of values

gene_expr=['gene', 5.16e-08, 0.001385, 7.33e-08]

Slice a list (it will create a new list)

gene_expr[-3:]  # [5.16e-08, 0.001385, 7.33e-08]
gene_expr[1:3] = [6.09e-07]

Clear the list


List functions

Size of the list


Delete an element

del gene_expr[1]

Extend/append to a list

gene_expr).extend([5.16e-08, 0.00123])

Count the number of times an element appears in a list

print(gene_expr.count('Lif'), gene_expr.count('gene'))

Reverse all elements in a list


Lists as Stacks

stack=['a', 'b', 'c', 'd']

Sorting lists

mylist=[3, 31, 123, 1, 5]
mylist  # not changed

mylist=['c', 'g', 'T', 'a', 'A']

Don't change an element in a string!

motif = 'nacggggtc'
motif[0] = 'a'    # ERROR


A tuple consists of a number of values separated by commas, and is another standard sequence data type, like strings and lists.

t=(1,2,3)  # we may input tuples with or without surrounding parentheses


A set is an unordered collection with no duplicate elements.

brca1={'DNA repair', 'zine ion binding'}
brca2={protein binding', 'H4 histone'}
brca1 | brca2
brca1 & brca2
brca1 - brca2


A dictionary is an unordered set of key and value pairs, with the requirement that the keys are unique (within on dictionary).

TF_motif = {'SP1' : 'gggcgg', 
            'C/EBP' : 'attgcgcaat',
            'ATF' : 'tgacgtca',
            'c-Myc' : 'cacgtg',
            'Oct-1' : 'atgcaaat'}
# Access
print("The recognition sequence for the ATF transcription is %s." % TF_motif['ATF']) 
# Update
TF_motif['AP-1'] = 'tgagtca'
# Delete
del TF_motif['SP1']
# Size of a list
# Get a list of all the 'keys' in a dictionary
# Get a list of all the 'values'
# sort

We can retrieve data from dictionaries using the items() method.

for name,seq in seqs.item():
    print(name, seq)

In summary, strings, lists and dictionaries are most useful data types for bioinformatics.

if statement

dna=input('Enter DNA sequence: ')
if 'n' in dna :
  print("dna sequence has %d undefined bases " % nbases)

if condtion 1:
  do action 1
elif condition 2:
  do action 2
  do action 3

Logical operators

Use and, or, not.

dna=input('Enter DNA sequence: ')
if 'n' in dna or 'N' in dna:
    print("dna sequence has %d undefined bases " % nbases)
    print("dna sequence has no undefined bases)



dna=input('Enter DNA sequence:')
pos=dna.find('gt', 0)

while pos>-1 :
    print("Donar splice site candidate at position %d" %pos)
    pos=dna.find('gt', pos+1)


motifs=["attccgt", "aggggggttttttcg", "gtagc"]
for m in motifs:
    print(m, len(m))


for i in range(4):
for i in range(1,10,2):

Problem: find all characters in a given protein sequence are valid amino acids.

for i in range(len(protein)):
    if protein[i] not in 'ABCDEFGHIKLMNPQRSTVWXYZ': 
        print("this is not a valid protein sequence!")


for i in range(len(protein)):
    if protein[i] not in 'ABCDEFGHIKLMNPQRSTVWXYZ': 
print("COrrected protein seq is %s" % corrected_protein)

else Statement used with loops

  • If used with a for loop, the else statement is executed when the loop has exhausted iterating the list
  • If used with a while loop, the else statement is executed when the condition becomes false
# Find all prime numbers smaller than a given integer
for y in range(2, N):
    for x in range(2, y):
        if y %x == 0:
            print(y, 'equals', x, '*', y//x)
            // loop fell through without finding a factor
            print(y, 'is a prime number')

The pass statement is a placeholder

if motif not in dna:


Get modular with Python function

def function_name(arguments) :
    return output

For example,

def gc(dna) :
    "this function computes the gc perc of a dna seq"
    return gcpercent

SyntaxError: invalid syntax

On the Python shell add an empty line at the end of function definition. Eg

>>> def fun(a):
...     return a+1
>>> fun(9)
>>> exit()

On a python script

def fun(a):
    return a+1
print fun(9)

Debug functions

You can launch a Python program through pdb by using pdb or python -m pdb

$ cat
def fun(a):
    a= a*2
    a= a*3
    return a+1
print fun(5)

$ python -m pdb
> /home/pi/Downloads/<module>()
-> def fun(a):
(Pdb) b fun
Breakpoint 1 at /home/pi/Downloads/
(Pdb) c
> /home/pi/Downloads/
-> a= a*2
(Pdb) n
> /home/pi/Downloads/
-> a= a*3
> /home/pi/Downloads/
-> return a+1
(Pdb) p a
(Pdb) n
> /home/pi/Downloads/>31
-> return a+1
(Pdb) exit

Boolean functions

Problem: checks if a given dna seq contains an in-frame stop condon

dna=input("Enter a dna seq: ")
if (has_stop_codon(dna)) :
    print("input seq has an in frame stop codon.")
else :
    print("input seq has no in frame stop codon.")

def has_stop_codon(dna) :
    "This function checks if given dna seq has in frame stop codons."
    stop_codons=['tga', 'tag', 'taa']
    for i in range(0, len(dna), 3) :
        if codon in stop_codons : 
    return stop_codon_found

Function default parameter values

Suppose the has_stop_codon function also accepts a frame argument (equal to 0, 1, or 2) which specifies in what frame we want to look for stop codons.

def has_stop_codon(dna, frame=0) :
    "This function checks if given dna seq has in frame stop codons."
    stop_codons=['tga', 'tag', 'taa']
    for i in range(frame, len(dna), 3) :
        if codon in stop_codons : 
    return stop_codon_found

has_stop_codon(dna)    # False
has_stop_codon(dna, 0) # False
has_stop_codon(dna, 1) # True
has_stop_codon(frame=0, dna=dna)

More examples

Reverse complement of a dna sequence

def reversecomplement(seq):
    """Return the reverse complement of the dna string."""
    seq = reverse_string(seq)
    seq = complement(seq)
    return seq


To reverse a string

def reverse_string(seq):
    return seq[::-1]


Complement a DNA Sequence

def complement(dna):
    """Return the complementary sequence string."""
    basecomplement = {'A':'T', 'C':'G', 'G':'C', 'T':'A', 
                      'N':'N', 'a':t', 'c':'g', 'g':'c', 't':'a', 'n':'n'} # dictionary
    letters = list(dna) # list comprehensions
    letters = [basecomplement[base] for base in letters]
    return ''.join(letters)

Split and Join functions

sentence="enzymes and other proteins come in many shapes"
sentence.split()  # split on all whitespaces
sentence.split('and') # use 'and' as the separator

'-'.join(['enzymes', 'and', 'other', 'proteins', 'come', 'in', 'many', 'shapes'])

Variable number of function arguments

def newfunction(fi, se, th, *rest):
  print("First: %s" % fi)
  print("Second: %s" % se)
  print("Third: %s" % th)
  print("Rest... %s" % rest)

Modules and packages

Packages group multiple modules under on name, by using "dotted module names". For example, the module name A.B designates a submodule named B in a package named A. See What's the difference between a Python module and a Python package?


dnautil module contains a few useful functions for dna seq
def gc(dna) :
    return gcpercent

When a module is imported, Python first searches for a built-in module with that name.

If built-in module is not found, Python then searches for a file obtained by adding the extension .py to the name of the module that it's imported:

  • in your current directory,
  • the directory where Python has been installed
  • in a path, i.e., a colon(':') separated list of file paths, stored in the environment variable PYTHONPATH.

You can use the sys.path variable from the sys built-in module to check the list of all directories where Python look for files

import sys

If the sys.path variable does not contains the directory where you put your module you can extend it:


Using modules (from PACKAGE/DIRNAME/FILENAME import CLASS)

from math import *

import dnautil
gc(dna)          # gc is not defined
dnautil.gc(dna)  # Good

Import Names from a Module

from dnautil import *
gc(dna)          # OK

from dnautil import gc, has_stop_codon

Get modular with Python functions & Learn object-oriented programming with Python from

from...import vs import vs

  • Difference between 'import' and 'from...import' in Python
  • Import, From and As Keywords in Python
  • `from … import` vs `import .`
  • Difference between import and from in Python. Python's import loads a Python module into its own namespace, so that you have to add the module name followed by a dot in front of references to any names from the imported module that you refer to:
    import feathers
    duster = feathers.ostrich("South Africa")

    from loads a Python module into the current namespace, so that you can refer to it without the need to mention the module name again:

    from feathers import *
    duster = ostrich("South Africa")
    • Question: Why are both import and from provided? Can't I always use from? Answer: If you were to load a lot of modules using from, you would find sooner or later that there was a conflict of names; from is fine for a small program but if it was used throughout a big program, you would hit problems from time to time
    • Question: Should I always use import then? Answer: No ... use import most of the time, but use from is you want to refer to the members of a module many, many times in the calling code; that way, you save yourself having to write "feather." (in our example) time after time, but yet you don't end up with a cluttered namespace. You could describe this approach as being the best of both worlds.
  • from … import OR import … as for modules
  • Some examples:
    from numpy import array   # Run file; load specific 'attribute'
    arr = array([1,2,3])    # Use name directly: no need to qualify
    print(arr) # print [1 2 3]
    from math import pi
    pi # 3.141592653589793
    math.pi  # NameError: name 'math' is not defined


    import numpy   # Run file; load module as a whole
    arr = numpy.array([1,2,3])  # Use its attribute names: '.' to qualify
    print(arr) # print [1 2 3]
    import math
    math.pi # 3.141592653589793


    import numpy as np
    import math as m
    m.pi # 3.141592653589793
  • scRNA_cell_deconv_benchmark example.


from AAA import BBB

import BBB as CCC

Packages &

Each package in Python is a directory which MUST contain a special file This file can be empty and it indicates that the directory it contains is a Python package, so it can be imported the same way a module can be imported.

Example: suppose you have several modules, , and You want to group them in a package called "bioseq" which processes all types of biological sequences. The structure of the package:


Loading from packages:

import bioseq.dnautil

from bioseq import dnautil

from bioseq.fasta.fastautil import fastqseqread


Building a Multiple Choice Quiz by

class Question:
    def __init__(self, prompt, answer):
        self.prompt = prompt
        self.answer = answer

from QuestionFile import Question

question_prompts = [
    "What color are apples?\n(a) Red/Green\n(b) Purple\n(c) Orange\n\n",
    "What color are Bananas?\n(a) Teal\n(b) Magenta\n(c) Yellow\n\n",
    "What color are strawberries?\n(a) Yellow\n(b) Red\n(c) Blue\n\n"

questions = [
    Question(question_prompts[0], "a"),
    Question(question_prompts[1], "c"),
    Question(question_prompts[2], "b")

def run_test(question):
    score = 0
    for question in questions:
        answer = input(question.prompt)
        if answer == question.answer:
            score += 1
    print("You got " + str(score) + " /" + str(len(questions))+ " correct")


Run the program by python3

Files - Communicate with the outside

f=open('myfile', 'r') # read
f=open('myfile', 'w') # write
f=open('myfile', 'a') # append

Take care if a file does not exists

    f = open('myfile')
except IOError:
    print("the file myfile does not exist!!")


for line in f:

Change positions within a file object  # go to the beginning of the file

Read a single line

Write into a file

f=open("/home/$USER/myfile, 'a)
f.write("this is a new line")

>>> with open("file.txt", "w") as f:
...   f.write(str(object))

Importing large tab-delimited .txt file into Python

# R
write.table(iris[1:10,], file="iris.txt", sep="\t", quote=F, row.names=F)

# Python
import csv
with open('iris.txt') as f:
    reader = csv.reader(f, delimiter="\t")
    d = list(reader)

# Shell
$ python

If the data are all numerical, we can use the numpy package.

# R
write.table(iris[1:10, 1:4], 
            sep="\t", quote=F, row.names=F, col.names=F)

# Python
import numpy as np
d = np.loadtxt('iris2.txt', delimiter="\t")

# Shell
$ python

Read text file from a URL

import urllib.request

url = ""
file = urllib.request.urlopen(url)

for line in file:

Command line arguments

Suppose we run 'python myfile.fa' in the command line, then

import sys
print(sys.argv)  #  ['', 'myfile.fa']

More completely

""" builds a dictionary with all sequences from a FASTA file.

import sys

  f = open(filename)
except IOError:
    print("File %s does not exist!" % filename)

Parsing command line arguments with getopt. Suppose we want to store in the dictionary the sequences bigger than a given length provided in the command line: ' -l 250 myfile.fa'

import sys
import getopt

def usage():
    print """ reads a FASTA file and builds a 
dictionary with all sequence bigger than a given length [-h] [-l <length>] <filename>

 -h           print this message
 -l <length>  filter all sequences with a length
              smaller than <length>
              (default <length>=0)
 <filename>   the file has to be in FASTA format

o, a = getopt.getopt(sys.argv[1:], '1:h')
opts = {} # empty dictionary

for k,v in o:
    opts[k] = v
if 'h' in opts.keys():  # he means the user wants help
    usage(); sys.exit()
if len(a) < 1:
    usage(); sys.exit("input fasta file is missing")
if 'l' in opts.keys():
    if opts['l'] <0 :
        print("length of seq should be positive!"); sys.exit(0);

stdin and stdout

sys.stdout.write("Some useful ouput.\n")

sys.stderr.write("Warning: input file was not found\n")

Call external programs

import subprocess'["ls", "-l"]) # return code indicates the success or failure of the execution'["tophat", "genome_mouse_idx", "PE_reads_1.fq.gz", "PE_reads_2.fq.gz"])


5 Python Examples to Handle Exceptions using try, except and finally


How to Debug Your Python Code

Biopython & Pubmed

  • Parsers for various bioinformatics file formats (FASTA, Genbank)
  • Access to online services like NCBI Entrez or Pubmed databases
  • Interfaces to common bioinformatics programs such as BLAST, Clustalw and others.
import Bio

Running BLAST over the internet

from Bio.Blast import NCBIWWW
fasta_string = open("myseq.fa").read()
result_handle = NCBIWWW.qblast("blastn":, "nt", fasta_string)
# blastn is the program to use
# nt is the database to search against
# default output is xml

The BLAST record

from Bio.Blast import NCBIXML
blast_record =

Parse BLAST output


for alignment in blas_record.alignments:
  for hsp in alignment.hsps:
    if hsp.expect < E_VALUE_THRESH:
      print('sequence:', alignment.title)
      print('length:', alignment.length)
      print('e value:', hsp.expect)

More help with Biopython


Parser for Pubmed Open-Access XML Subset and MEDLINE XML Dataset


pyc file

What is the difference between .py and .pyc files? [duplicate]. I observe it can cause a problem when I want to modify a python file but it keeps using the old pyc file so my change is not used (Raspbery Pi e-ink example).

Shutdown or restart OS

Below is tested on Raspbian

import os
os.system('sudo shutdown -h now')

Popular python libraries

20 Python libraries you can’t live without


# pip install psutil --user
for x in range(10):



30 pandas Commands for Manipulating DataFrames

Write a pandas dataframe to a text file using to.csv().

a.to_csv('xgboost.txt', header=True, index=True, sep='\t')





python -m pip install -U pip
python -m pip install -U matplotlib

sudo apt-get install python3.5-tk


from sklearn import datasets
iris = datasets.load_iris()
import matplotlib.pyplot as plt
iris =

# Scatterplot
plt.scatter(iris[:,1], iris[:,2])

# Boxplot

# Histogram


scikit-learn: Machine Learning in Python


pip install -U scikit-learn


$ python
>>> from sklearn import datasets
>>> iris = datasets.load_iris()
>>> digits = datasets.load_digits()



Never miss a Magazine article — build your own RSS notification system


A Python interface to Amazon Web Services

PIL, Pillow


Python and R – Part 2: Visualizing Data with Plotnine

nltk: Natural Language Toolkit


Learn Python by creating a video game


Trouble shooting

ImportError: cannot import name main when running pip

Error: externally-managed-environment

See pipx

TypeError: ‘module’ object is not callable

I was trying to run "" from here.

Solve “TypeError: ‘module’ object is not callable” in Python, TypeError: 'module' object is not callable

The problem is I have a file called "" and I have "import bbknn" in the code. It will confuse python. The solution is to rename my script file "" (avoid to other name like "".

When I import my module in python, it automatically runs all of the defined functions inside of it. How do I prevent it from auto executing my functions, but still allow me to call them in my main script?

Illegal instruction

I got this error after I called python3 -c 'import scanpy'. Python on Biowulf.

TMPDIR=/tmp bash -p ~/conda -b

source ~/conda/etc/profile.d/ # ~/conda/condabin is added to PATH

conda activate base
python -V # Python 3.9.4

conda create -n project1 pandas numpy scipy -y
conda activate project1
pip3 install scanpy bbknn
ls ~/conda/envs/project1/lib/python3.9/site-packages
# bbknn and scanpy are there  
python3 -c 'import scanpy'
# Illegal instruction

conda info --env
conda deactivate
conda remove --all -n project1 -y
conda deactivate

No matching distribution found for XXX

Got an error No matching distribution found for lasagne==0.2.dev1 when I ran 'pip install .' on DeepSurv.

Python AttributeError: 'module' object has no attribute 'SSL_ST_INIT'

See I got this message after I ran sudo pip install --upgrade cryptography and pip show cryptography. The reason I try to upgrade cryptography is the following message

$ pip show protobuf
  RequestsDependencyWarning: Old version of cryptography ([1, 2, 3]) may cause slowdown.
  warnings.warn(warning, RequestsDependencyWarning)
Name: protobuf

And OpenSSL & pyOpenSSL-0.15.1.egg-inf are under /usr/lib/python2.7/dist-packages directory on my Ubuntu 16.04.

Note the following solutions do not work

$ sudo pip uninstall pyopenssl
$ sudo pip install pyOpenSSL==16.2.0

I always get an error message

  File "/usr/lib/python2.7/dist-packages/OpenSSL/", line 118, in <module>
AttributeError: 'module' object has no attribute 'SSL_ST_INIT'

And a quick solution is to do sudo rm -r /usr/local/lib/python2.7/dist-packages/OpenSSL. I also did sudo pip install pyopenssl but I did not follow this answer (sudo apt install --reinstall python-openssl).

/usr/bin/env: ‘python’: No such file or directory

On Ubuntu 20.04,

sudo apt-get install python-is-python3

This solved an error when I used youtube-dl.

Projects based on python

  • pithos Pandora on linux
  • Many Raspberry Pi GPIO projects
  • GeneScissors It also requires pip and scikit-learn packages.
  • KeepNote It depends on Python 2.X, sqlite and PyGTK.
  • Zim It depends on Python, Gtk and the python-gtk bindings.
  • Cherrytree It depends on Python2, Python-gtk2, Python-gtksourceview2, p7zip-full, python-enchant and python-dbus.

Send emails

  • Less secure apps & your Google Account. To help keep your account secure, from May 30, 2022, ​​Google no longer supports the use of third-party apps or devices which ask you to sign in to your Google Account using only your username and password.
    • Send Email via Gmail and SMTP Use an App Password 2022/9. Click on Security -> 2-Step Verification (You may need to enter your PW first). Scroll to the bottom of the page, and you'll see the "App passwords" section. You can delete/create app passwords but you can't view any existing passwords.
  • How to Send Automated Email Messages in Python 3 2021/3

GUI programming

New book: Create Graphical User Interfaces with Python

Qt for GUI development

Python 3


Use pip3 instead of pip for Python 3. For example,

pip3 install --upgrade pip

pip3 install -U scikit-learn

pip3 install -U matplotlib


Edit Files With Workspaces. The 'http.server' module is contained in python3.

cd ~/website
python3 -m http.server

C vs Python

C vs. Python: The Key Differences

R and Python: reticulate package

  • Installing and Configuring Python with RStudio
    • The instruction is based on virtualenv. But I'm following Biowulf's Python miniconda instruction to create a new project/environment. One caveat is I need to run source ~/$USER/conda/etc/profile.d/ each time before I start R in order to make conda available OR I need to set the RETICULATE_MINICONDA_PATH variable (see below).
    • The conda-related reticulate functions include conda_create(), use_condaenv(), conda_install(), conda_list(), conda_remove()
    • Use py_config() to check the current python path and other python versions found.
    • My example
      # Assume I followed Biowulf's instruction to create 'project1'
      Sys.setenv(RETICULATE_MINICONDA_PATH = "~/conda") 
      use_condaenv("project1", required=T)
  • Python Version Configuration. Suppose I have installed miniconda and create a new environment called 'project1'. Then after calling source ~/conda/etc/profile.d/ I can start in R
    use_condaenv("project1", required = TRUE)
  • Test python and markdown files
    def add_three(x):
        z = x + 3
        return z
    title: "R Notebook"
    output: html_notebook
    x <- 5
    y <- add_three(x)
    Pass R variables to Python. Works
    a = 7
    Pass python variables to R. Works.
    py_run_string("y = 10"); py$y

How to quit python

Type exit and hit Enter. See

R vs Python

Call R from Python

  • rwrap Seamlessly integrate R packages into Python.
  • rpy2

Conda, Anaconda, miniconda

Private environment

Conda on Biowulf & mambaforge

Transfer a conda environment to another computer: YAML files

Managing environments

# computer 1
conda env export > environment.yml

# computer 2
conda env create -f environment.yml


  • Introduction to Anaconda. Simplifies installation of Python packages
    • Platform-independent package manager
    • Doesn’t require administrative privileges
    • Installs non-Python library dependencies (MKL, HDF5, Boost)
    • Provides ”virtual environment” capabilities
    • Many channels exist that support additional packages
  • Install Anaconda on macOS. Better to use the command line method in order to install it to the user's directory. The new python can be manually loaded into the shell by using source ~/.bash_profile. Like Ubuntu, ananconda3 is installed under ~/ directory. In addition, Anaconda-Navigator is available under Finder -> Applications.
  • How To Install the Anaconda Python Distribution on Ubuntu 16.04. As we can see Anaconda3 will be installed under /home/$USER/anaconda3.
    • Download from
    • bash
    • There is a question: Do you wish the installer to initialize Anaconda3. If you answer Yes, it will run conda init & modify ~/.bashrc file. # This will overwrite system's Python. So the default python/python3 will now be in /home/$USER/anaconda3/bin/.
      Do you wish the installer to initialize Anaconda3
      by running conda init? [yes|no]
      [no] >>> yes
      no change     /home/brb/anaconda3/condabin/conda
      no change     /home/brb/anaconda3/bin/conda
      no change     /home/brb/anaconda3/bin/conda-env
      no change     /home/brb/anaconda3/bin/activate
      no change     /home/brb/anaconda3/bin/deactivate
      no change     /home/brb/anaconda3/etc/profile.d/
      no change     /home/brb/anaconda3/etc/fish/conf.d/
      no change     /home/brb/anaconda3/shell/condabin/Conda.psm1
      no change     /home/brb/anaconda3/shell/condabin/conda-hook.ps1
      no change     /home/brb/anaconda3/lib/python3.8/site-packages/xontrib/conda.xsh
      no change     /home/brb/anaconda3/etc/profile.d/conda.csh
      modified      /home/brb/.bashrc
      ==> For changes to take effect, close and re-open your current shell. <==
      If you'd prefer that conda's base environment not be activated on startup, 
         set the auto_activate_base parameter to false: 
      conda config --set auto_activate_base false

      If I choose not to modify .bashrc file,

      Do you wish the installer to initialize Anaconda3
      by running conda init? [yes|no]
      [no] >>> no
      You have chosen to not have conda modify your shell scripts at all.
      To activate conda's base environment in your current shell session:
      eval "$(/home/brb/anaconda3/bin/conda shell.YOUR_SHELL_NAME hook)" 
      To install conda's shell functions for easier access, first activate, then:
      conda init
      If you'd prefer that conda's base environment not be activated on startup, 
         set the auto_activate_base parameter to false: 
      conda config --set auto_activate_base false
      Thank you for installing Anaconda3!
    • Anaconda-Navigator (including jupyter notebook, Spyder IDE, ...) can be launched by typing anaconda-navigator in a terminal
conda --version

# Manage environment
conda info --envs  # see a list of environments. 
                   # The active environment is the one with an asterisk (*)
# create a new environment
conda create --name myenv
# remove an environment
conda remove --name myenv --all

# Manage Python
conda create --name snakes python=3.5
conda activate snowflakes # activate
conda info --envs
python --version
conda activate  # Change your current environment back to the default (base)
conda deactivate # exit any python virtualenv

# Managing packages
conda search beautifulsoup4
conda install beautifulsoup4
conda list

# Updating Anaconda or Miniconda
conda update conda


  • As you can see miniconda installers were separated by the Python version.
  • How To Install Miniconda In Linux 2021. It includes Install Miniconda interactively, unattended installation, Update Miniconda, and Uninstall Miniconda. If you've chosen the default location, the installer will display “PREFIX=/var/home/<user>/miniconda3”. To manually activate conda's base environment, do /home/<user>/miniconda3/etc/profile.d/ where we assume miniconda is installed under /home/<user>/miniconda3 directory.
  • Miniconda Installation for macOS users 2019. At the end of installation, we see if we don't want conda's base environment to be activated on start up, we can do conda config --set auto_activate_base false
  • See also Python on Biowulf about how to specify prefix.
  • We can add/install a module to an existing environment. See Miniconda: Python(s) in a convenient setup.
conda install -n <env_name> <package>
conda create -n myenv python=3 # create a new environment named “myenv” with Python 3 installed
   # after that, use "conda activate myenv" and use "conda install numpy" to install the numpy

Install and "conda init"

  • Windows: screenshots are included Setting up Python on Windows with Miniconda by Anaconda & Anaconda documentation. The default is not to add Anaconda to my PATH environment variable.
  • Ubuntu: How to Install Miniconda on Ubuntu 20.04. After installation, PATH variable will prepend ~/miniconda3/condabin which contains only 1 file: conda.
  • conda init
    • Running conda init initializes conda for shell interaction by writing some shell code in the relevant startup scripts of your shell (e.g~/.bashrc) 1. This allows the conda command to interact more closely with the shell context and provides a cleaner PATH manipulation and snappier responses in some conda commands. The main advantage of running conda init is that it enables the use of the conda activate and conda deactivate commands, which are used to activate and deactivate conda environments.
    • One disadvantage of running conda init is that it can sometimes cause issues if the initialization is not done correctly or if there are conflicts with other configurations in your shell startup scripts. However, these issues can usually be resolved by troubleshooting and making the necessary changes to your configuration.

Install all anaconda packages

Uninstall miniconda

  1. rm -rf ~/miniconda3
  2. nano ~/.bash_profile and delete conda initialize block

What's the purpose of the “base” (for best practices) in Anaconda?

Does Conda replace the need for virtualenv?

Yes. Conda is not limited to Python but can be used for other languages too.


  • conda install gcc
  • Using conda-forge channel - conda install -c conda-forge gfortran

Using R language with Anaconda

  • Using R language with Anaconda
    conda create -n r_env r-essentials r-base
    conda activate r_env
  • Difference of install a package using install.packages() function in R and using the conda install command?
    • The install.packages() function in R and the conda install command are two different ways to install R packages. The install.packages() function is used to install packages from the Comprehensive R Archive Network (CRAN), while the conda install command is used to install packages from the Anaconda repository.
    • One key difference between the two methods is that conda can manage dependencies across multiple programming languages, while install.packages() only manages dependencies within R.
    • Another difference is that conda allows you to create and manage multiple isolated environments, each with its own set of packages. This can be useful if you want to have different versions of packages available for different projects. With install.packages(), all packages are installed in the same global library, which can make it more difficult to manage dependencies and avoid conflicts.
  • The Definitive Guide to Conda Environments, Using R language with Anaconda. Environments created with conda create live by default in the envs/ folder of your Conda directory, whose path will look something like /Users/user-name/miniconda3/envs or /Users/user-name/anaconda3/envs.
    Activate conda base                  Create a new env    Activate a new env           Deactivate an env
    ----------------------------> (base) ----------------->  -------------------> (r-env) -----------------> (base)
    eval $(conda shell.bash hook)"       conda create r-env  conda activate r-env         conda deactivate
    $ eval "$(/home/brb/anaconda3/bin/conda shell.bash hook)"
    (base) $ mkdir mypythonproj; cd mypythonproj  # This step seems not necessary
    (base) $ conda create -n r-env r-base
    # To activate this environment, use
    #     $ conda activate r-env
    # To deactivate an active environment, use
    #     $ conda deactivate
    (base) $ conda activate r-env
    (r-env) $ ls anaconda3/envs
    (r-env) $ conda install r-essentials
    (r-env) $ which R
    (r-env) $ ls -la   # Still Empty
    (r-env) $ R --version
    R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
    # Note that the current R version should be 4.0.3
    (r-env) $ conda env list
    base                     /home/brb/anaconda3
    r-env                 *  /home/brb/anaconda3/envs/r-env
    (r-env) $ conda deactivate
    (base)  $ 

    It seems to be better to save the environment inside a project directory. So using python -m venv /path/to/new/environment method is preferred. You can also use conda create --prefix /path/to/new/environment. Placing environments outside of the default env/ folder comes with some drawbacks. Read the document of 'The Definitive Guide to Conda Environments'.

  • conda-forge channel, A brief introduction, Following the instruction seems to mess things up though the conda-forge says the latest version is 4.0.3 (3 years late).
    $ eval "$(/home/brb/anaconda3/bin/conda shell.bash hook)"
    (base) $ conda install -c conda-forge r-base
    ## Package Plan ##
      environment location: /home/brb/anaconda3
      added / updated specs:
        - r-base
    Downloading and Extracting Packages
    r-base-3.2.2    ...
    (base) $ R --version
    /home/brb/anaconda3/lib/R/bin/exec/R: error while loading shared libraries: cannot open shared object file: No such file or directory
    (base) $ which R

Run R with Jupyter notebook

Example 1: GEO2RNAseq


Example 2: p-NET

Biologically informed deep neural network for prostate cancer classification and discovery and the paper 2021.


Web framework




Simulate gravity in your Python game