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Bioinformatics Programming

How to commit changes to GitHub repository using vs code?

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How to commit changes to GitHub repository using vs code?

In this article, we are providing a few commands that are used to commit changes to GitHub repositories using VS code terminal.

Committing changes for the first time

For committing changes for the first time, follow these steps:

  • Open VS code –> go to Terminal.
  • Clone your GitHub repository.
    Go to your desired directory where you want to clone the repository and paste the following command:
    $ git clone <url-to-repository>
  • Now make all changes you want.
  • After that, run the following command:
    $ git add .
    Here, the dot (.) refers to all folders.
  • Now, commit changes with a message:
    $ git commit -m "write something here"
  • Push all changes to the repository.
    $ git push
  • Now, refresh your GitHub repository, you will be able to see all changes there.

Committing further changes

If you have already committed any changes before, then you don’t need to clone your repository again. Make changes and then commit and push as shown above.


 

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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Bioinformatics Programming

How to make swarm boxplot?

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How to make swarm boxplot?

With the new year, we are going to start with a very simple yet complicated topic (for beginners) in bioinformatics. In this tutorial, we provide a simple code to plot swarm boxplot using matplotlib and seaborn. (more…)

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Bioinformatics Programming

How to obtain ligand structures in PDB format from PDB ligand IDs?

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How to obtain ligand structures in PDB format from PDB ligand IDs?

Previously, we provided a similar script to download ligand SMILES from PDB ligand IDs. In this article, we are downloading PDB ligand structures from their corresponding IDs. (more…)

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Bioinformatics Programming

How to obtain SMILES of ligands using PDB ligand IDs?

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How to obtain SMILES of ligands using PDB ligand IDs?

Fetching SMILE strings for a given number of SDF files of chemical compounds is not such a trivial task. We can quickly obtain them using RDKit or OpenBabel. But what if you don’t have SDF files of ligands in the first place? All you have is Ligand IDs from PDB. If they are a few then you can think of downloading SDF files manually but still, it seems time-consuming, especially when you have multiple compounds to work with. Therefore, we provide a Python script that will read all Ligand IDs and fetch their SDF files, and will finally convert them into SMILE strings. (more…)

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