#!/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');
