Bioinformatics Programming
Extract FASTA sequences based on sequence length using Perl
Here are simple Perl scripts to filter out FASTA sequences from a multi-fasta file based on sequence length.
Let’s say our input file consisting of multiple FASTA sequences is ‘input.fasta’.
#!/usr/bin/perl
use strict;
use warnings;
my ($infile, $minlen) = @ARGV;
{
local $/=">";
while(<$infile>) {
chomp;
next unless /\w/;
my @keep = split /\n/;
my $header = shift @keep;
my $seqlen = length join "", @keep;
if($seqlen >= $minlen){
print ">$_";
}
}
local $/="\n";
}
exit;
Save this Perl script as ‘extractfasta.pl‘ and run in the terminal as
$ perl extractfasta.pl input.fasta <minlen> > output.fasta
For example,
$ perl extractfasta.pl input.fasta 100 > output.fasta
If you want to set a maximum length limit as well, then use the following script.
#!/usr/bin/perl
use strict;
use warnings;
my ($infile, $minlen, $maxlen) = @ARGV;
{
local $/=">";
while(<$infile>) {
chomp;
next unless /\w/;
my @keep = split /\n/;
my $header = shift @keep;
my $seqlen = length join "", @keep;
if($seqlen >= $minlen){
print ">$_";
}
}
local $/="\n";
}
exit;
Save this Perl script as ‘extractfasta.pl‘ and run in the terminal as
$ perl extractfasta.pl input.fasta <minlen> <maxlen> > output.fasta
For example,
$ perl extractfasta.pl input.fasta 100 350 > output.fasta
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…)
[email protected]
April 13, 2021 at 3:52 am
I got an error when usong the second command:
readline() on unopened filehandle at extractfasta.pl line 7
this is what I run:
perl extractfasta.pl /path-to/BAC4A_L00M_R1_001.fasta 50 100 > 100_maxln.fasta
the input fasta is ok , dont know what is wrong ):