Not a very good translation of: 

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       n
+othing 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;

[download]


my(@lines) = '/tmp/zea_mays.txt';

[download]

Why store a scalar value in an array? 

while ( defined( my $line = readline \*IN ) ) {
    do {
        foreach $line (@lines) {

[download]

And then here you loop through that single value, a file name, and ignore the lines read from the file.    And what's up with the superfluous do block? 



                my (@peptides) = split( /(?<=RK(?!P))/, $line );

[download]

The original used the character class [RK] but you are using the string RK?

In reply to Re^2: First header missing from FASTA data by Anonymous Monk
in thread First header missing from FASTA data by bugiep

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