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");
Bioinformatics Programming
sminalog_analysis.py – A new Python script to fetch top binding affinities from SMINA log file
In one of our previous posts, we provided a Python script for the virtual screening analysis of Autodock Vina. This script analyzes all log files obtained from docking of multiple ligands to a receptor and provides the binding affinities for top poses from each file. In this article, we are publishing a new Python script for the virtual screening analysis of SMINA [1]. (more…)
Pycharm [1] is an integrated development environment (IDE) for developers. It combines Python developer tools and provides an easy graphical user interface. In this article, we are going to install Pycharm on Ubuntu. (more…)
The output files obtained as a result of virtual screening (VS) using Autodock Vina may be large in number. It is difficult or quite impossible to analyze them manually. Therefore, we are providing a Python script to fetch top results (i.e., compounds showing low binding affinities). (more…)
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