Perl script to convert Multi-line Fasta to Single-line Fasta !

BioStar — Wed, 31 Jan 2024 00:38:21 -0600

#!/usr/bin/perl

use strict;
use warnings;

sub multi_to_single_line_fasta {
    my ($input_filename, $output_filename) = @_;

    open my $input_file, '<', $input_filename or die "Error: Could not open file '$input_filename': $!";
    open my $output_file, '>', $output_filename or die "Error: Could not open file '$output_filename': $!";

    my $current_sequence = "";

    while (my $line = <$input_file>) {
        chomp $line;
        if ($line =~ /^>/) {
            # If a header line, write the previous sequence and then the new header
            print $output_file $current_sequence . "\n" if $current_sequence;
            print $output_file $line . "\n";
            $current_sequence = "";
        } else {
            # If a sequence line, concatenate to the current sequence
            $current_sequence .= $line;
        }
    }

    # Write the last sequence
    print $output_file $current_sequence . "\n" if $current_sequence;

    close $input_file;
    close $output_file;

    print "Successfully converted $input_filename to $output_filename in single-line FASTA format.\n";
}

# Example usage:
# multi_to_single_line_fasta('multi_line.fasta', 'single_line.fasta');

BOL: Perl script to convert Multi-line Fasta to Single-line Fasta !

Perl script to convert Multi-line Fasta to Single-line Fasta !