Bioinformatics Programming
A perl script to convert multiline FASTA sequences into a single line

There are different software or tools which require different kinds of input, especially, when you are trying to developing a pipeline or want to process multiple large files.
If you are dealing with a big FASTA file consisting of thousands of sequences split into a particular number of residues per line, and you want each sequence into a single line, then you can use this simple Perl program.
There are two cases to input your multiline fasta file, either you define the filename in your Perl script or get it through the command line.
1. Define input file within the script
The multifasta input file is “input.fasta”.
#!/usr/bin/perl use strict; use warnings; my $input_fasta = "input.fasta"; open(IN,"<", "input_fasta") || die ("Can't open $input_fasta $!"); my $line = <IN>; print $line; while ($line = <IN>) { chomp $line; if ($line=~m/^>/gi) { print "\n",$line,"\n"; } else { print $line; } } print "\n";
2. As a command-line argument
#!/usr/bin/perl use strict; use warnings; my $input_fasta = $ARGV[0]; open(IN,"<", "$input_fasta") || die ("Can't open $input_fasta $!"); my $line = <IN>; print $line; while ($line = <IN>) { chomp $line; if ($line=~m/^>/gi) { print "\n",$line,"\n"; } else { print $line; } } print "\n";
Bioinformatics Programming
tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of multiple compounds

We previously provided a Python script to calculate the Tanimoto similarities of multiple compounds against each other. In this article, we are providing another Python script to calculate the Tanimoto similarities of one compound with multiple compounds. (more…)
Bioinformatics Programming
tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.

RDKit [1] is a very nice cheminformatics software. It allows us to perform a wide range of operations on chemical compounds/ ligands. We have provided a Python script to perform fingerprinting using Tanimoto similarity on multiple compounds using RDKit. (more…)
Bioinformatics Programming
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.
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