Bioinformatics Programming
How to execute Unix/shell commands in PHP?
Besides, Python & Perl, PHP is another language mostly used in bioinformatics programming. In this article, we provide a simple command to execute shell commands in a PHP script.
shell_exec()
It runs command via shell and returns the output as a string.
syntax: $output = shell_exec($command);
If you are using variables inside your command, you need to use escapeshellarg().
syntax: $output = shell_exec($command);
Let’s assume, if you are running the blastp command on a query file with a variable filename, then it could be run like this:
$output = shell_exec("blastp -query ".escapeshellarg($filename.'.fasta')." -db /path/to/db -out output.txt");
In this article, we are providing a few commands that are used to commit changes to GitHub repositories using VS code terminal.
The x, y, and z coordinates of atoms are provided in the PDB file. One way to extract them is by using the Biopython package [1]. In this article, we will extract coordinates of C-alpha atoms for each residue from the PDB file using Biopython. (more…)
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