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
AlgorithmsBioinformatics ProgrammingPerl

How to read fasta sequences as hash using perl?

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

This is a simple Perl script to read a multifasta file as a hash.

Suppose, your multifasta file is “input.fasta”, which you want to read as the hash.

#! /usr/bin/perl
use warnings;
use strict;
my $infile = "input.fasta";
my %sequences;

open( FH, '<', $infile ) or die $!;

while( my $line = <FH> ){
      chomp $line;
      if ( $line =~ /^(>.*)$/ )){
           my $id = $1;
      }
      elseif ( $line !~ /^\s*$/ ){
           $sequences{$id} .= $line;
      }
}

close (FH);
exit;

If you want to write a subroutine for reading a fasta file, then you can do like this:

#! /usr/bin/perl
use warnings;
use strict 'vars';

my $infile = "input.fasta";
my %seqs = %{ read_fasta_as_hash($infile) };#call the subroutine
          #your code goes here

sub read_fasta_as_hash{
  my $inputfile = shift;
  my $id = '';
  my %sequences;
  open( INFILE, '<', $inputfile ) or die $!;
        
  while( my $line = <INFILE> ){ 
        chomp $line;
        if ( $line =~ /^(>.*)$/ )){
            my $id = $1;
        }
        elseif ( $line !~ /^\s*$/ ){
             $sequences{$id} .= $line;
        }
   }
   close (INFILE);
   return %sequences;
}

exit;
TAGGED:FastaPerl
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

smitostr.py: Python script to convert SMILES to structures.
Bioinformatics ProgrammingCheminformaticsPython

smitostr.py: Python script to convert SMILES to structures.

November 19, 2022
How to commit changes to GitHub repository using vs code?
Bioinformatics ProgrammingGitHub

How to commit changes to GitHub repository using vs code?

February 28, 2024
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 Programming

Modifying multi-FASTA files using Bash: ‘Sed’ Command

July 18, 2020
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