Hello everyone, the editor is here to answer the following questions for you. Do you need to download pycharm to download python? Does it cost money to download and install python software? Let’s take a look today!
Purpose: Learn Python-based bioinformatics data processing. All work here is done on MacOSpython simple pattern code.
Note 1: Installation of Python running environment
Anaconda is a free Python running platform. Download and install it from the official website: https://www.anaconda.com/. The Jupyter Notebook in the program is a very good application for learning python and can be used to take notes and run python code.
When writing Python code, it is recommended to use PyCharm (or Vim). Using a txt editor will have some hidden formatting problems. PyCharm download address: https://www.jetbrains.com/pycharm/. PyCharm is a paid software, but you can choose a trial. You can continue to use it after expiration, but the software will restart every 30 minutes. Since the software automatically saves the data, you can continue to use it.
Bioconda is a platform that can easily install many bioinformatics packages, and I chose to use it for data analysis. Bioconda is a Channel under Conda. Before choosing to install Bioconda, you need to install Conda. Since Conda is part of Anaconda, you do not have to install Conda if Anacoda is already installed, otherwise you need to install Minicoda. Miniconda is the name of Conda's installation package to distinguish it from Anaconda.
Installation method: Run the following codes in MacOS Terminal. The latter two are to install r and conda-forge respectively.
conda config --add channels bioconda
conda config --add channels r
conda config --add channels conda-forge
Check whether the installation is successful: Open Anaconda, and you can see the installed Channel under Environments - Channels, as follows:
Use code to view all Channels: In Home - Jupyter Lab, enter the Console, enter the following code, and press Shift + Enter (you may only need to enter in other places)
conda config --show channels
View all Packages: In the Console, enter and execute the code: conda list
When you want to use a package, write import package_name at the beginning of the code. For example, after installing Bioconda, the system automatically installs the numpy package. We use it and check its version information. code show as below:
import numpy as np
print(np.__version__)
#Here import as can temporarily modify the package name for easy use below.