Bioinformatics ReviewBioinformatics Review
Notification Show More
Font ResizerAa
  •  Home
  • Docking
  • MD Simulation
  • Tools
  • More Topics
    • Softwares
    • Sequence Analysis
    • Algorithms
    • Bioinformatics Programming
    • Bioinformatics Research Updates
    • Drug Discovery
    • Phylogenetics
    • Structural Bioinformatics
    • Editorials
    • Tips & Tricks
    • Bioinformatics News
    • Featured
    • Genomics
    • Bioinformatics Infographics
  • Community
    • BiR-Research Group
    • Community Q&A
    • Ask a question
    • Join Telegram Channel
    • Join Facebook Group
    • Join Reddit Group
    • Subscription Options
    • Become a Patron
    • Write for us
  • About Us
    • About BiR
    • BiR Scope
    • The Team
    • Guidelines for Research Collaboration
    • Feedback
    • Contact Us
    • Recent @ BiR
  • Subscription
  • Account
    • Visit Dashboard
    • Login
Font ResizerAa
Bioinformatics ReviewBioinformatics Review
Search
Have an existing account? Sign In
Follow US
Bioinformatics Programming

How to extract fasta sequences from a multi-fasta file based on matching headers in a separate file?

Tariq Abdullah
Last updated: May 20, 2020 5:48 pm
Tariq Abdullah
Share
1 Min Read
SHARE

This is a simple Perl script to extract FASTA sequences from a large fasta file depending on the matching fasta headers present in another file.

For example, your fasta sequences are present in a file named, “input.fa” and the headers are in another file called “headers.txt”.

#! /usr/bin/perl
use warnings;
use strict;
my $headerfile = 'headers.txt';
my $input = 'input.fa';
open( HEADERFILE, '<', $headerfile ) or die $!;
chomp ( my @headers = map { split } <$headerfile> );    #splitting lines on whitespaces.
close HEADERFILE;
my %seqs;
open( INPUTFILE, '<', $input ) or die $!;
{
local $/ = '';         #Reading until blank line
while ( <$input> ) {
     my ( $header, $sequence ) = m/>\s*(\S+)\n(.*)/ms;
     $sequences{$header} = $sequence;
}
open( my $seqsfile, ">", "input.fa" );
foreach my $header (@headers) {
             if ( $sequences{$header} ) {
                       print $header, "\n";
                       print $sequences{$header}, "\n";
             }
}

close( $seqsfile );
}

close INPUTFILE;
exit;
TAGGED:headeridsmultifastaPerlsequences
Share This Article
Facebook Copy Link Print
ByTariq Abdullah
Tariq is founder of Bioinformatics Review and Lead Developer 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.
Leave a Comment

Leave a Reply Cancel reply

You must be logged in to post a comment.

Starting in Bioinformatics? Do This First!
Starting in Bioinformatics? Do This First!
Tips & Tricks
[Editorial] Is it ethical to change the order of authors’ names in a manuscript?
Editorial Opinion
Installing bbtools on Ubuntu
[Tutorial] Installing BBTools on Ubuntu (Linux).
Sequence Analysis Software Tools
wes_data_analysis Whole Exome Sequencing (WES) Data visualization Toolkit
wes_data_analysis: Whole Exome Sequencing (WES) Data visualization Toolkit
Bioinformatics Programming GitHub Python

You Might Also Like

How to get secondary structure of multiple PDB files using DSSP in Python?
Bioinformatics ProgrammingPython

How to get secondary structure of multiple PDB files using DSSP in Python?

December 5, 2022
Bioinformatics ProgrammingPython

dssp_parser: A new Python package to extract helices from DSSP files.

May 10, 2022
VS_Analysis: A Python package to perform post-virtual screening analysis
Bioinformatics NewsBioinformatics ProgrammingGitHubPythonSoftwareToolsVirtual Screening

VS_Analysis: A Python package to perform post-virtual screening analysis

February 27, 2025
Installing pycharm on Ubuntu
Bioinformatics ProgrammingPythonSoftwareTools

Installing Pycharm on Ubuntu (Linux)

May 26, 2021
Copyright 2024 IQL Technologies
  • Journal
  • Customer Support
  • Contact Us
  • FAQs
  • Terms of Use
  • Privacy Policy
  • Cookie Policy
  • Sitemap
Welcome Back!

Sign in to your account

Username or Email Address
Password

Lost your password?

Not a member? Sign Up