Hi Everyone,

I am doing a regex on my FASTA data which contains multiple protein sequences and their description as a header line. My output should consist of a header line and the sequence. When i print it to FILE my first header is missing. all other header lines are present. Any insight would be very welcome. below is my perl script: 

use strict; 
use warnings;
 
open IN, "zea_mays.txt";
open OUT, ">zea_mays1.txt";
my @peptides; 
my $seq;
my $flag = 0;
while(my $line = <IN>){
    chomp($line);  #check the chomp function
    if ($line =~ /^>/) {
        if ($flag == 0){ #the first protein entry, which means nothing
+ in the memory to do
            $flag = 1;
            next; 
        }
        print "\n";
        print OUT " $line\n ";
    }else {
        $line =~ s/\s//g;
        my @peptides  = split(/(?<=[RK](?!P))/,$line);
        print OUT "@peptides\n";
        
    }
}
close IN;
close OUT;

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In reply to First header missing from FASTA data by bugiep

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