I do not have any special script to post here, nor any special output. This is a peculiar behavior by Perl, and I will talk about it in detail. I have an innocent print statement in a perl code, that is behaving badly. I am reading a plain text file line by line, adding some information to it, and printing the new line into output file. The total number of lines in unput files is 240303 and that in output file is 240063. Thus, a small fraction of lines were unexpectedly not present in output file. I found out which lines were missing, and asked the Perl script to take a pause when it has finished printing one of those missing lines. I could clearly see that the output file HAD that line, though improperly terminated. It didnt have the "\n", and some characters in the end of the file were missing. I did this many times, and the same characters were missing every time. But then, when I let the Perl script finish its job reading the whole input file and opened the output file, the line that was there before was missing, and its place (identified by its line number in the output file) was taken by the next line. This happened every time. This is not a very well-written script.. but still, writing down what i did, to give you an idea. 
#!/usr/bin/perl
use strict;
use warnings;

my $microsats = $ARGV[0];
my $orths = $ARGV[1];
open (MIC,"<$microsats") or die "Cannot open file $microsats: $!";
open (ORTHS,">$orths") or die "Cannot open file $orths: $!";

my %starthash=();
my %preused = ();

my $startcord = 5;
my $endcord = 7;
# example of input line:
# "NA1182988952620.b.scf     dinucleotide    AG    555    65    6000  
+  :    6002    a-g"

while (my $line = <MIC>){
    chomp $line;
    my @fields = split(/\t/,$line);
    push @{$starthash{$fields[$startcord]}} , $line;
}

while (my $line = <MIC>){
    chomp $line;
    next if exists $preused{$line};
    $preused{$line} = 1;
    my @fields = split(/\t/,$line);
    my @finalstatement = ();
    push @finalstatement, $line;
    
    my $searchstart = $fields[$startcord]-1;
    my $searchend = $fields[$endcord]+1;
    
    my $printer =0;
    $printer = 1 if $searchstart <= 1297 && 1297 <= $searchend; # turn
+ing $printer on at a line that is having the stated problem
    
    for (my $i = $searchstart; $i<= $searchend; $i++){
    
        if (exists $starthash{$i}){
            my @orthologous = @{$starthash{$i}};
            delete $starthash{$i};             
    
            foreach my $single (@orthologous){
                next if exists $preused{$single};
                $preused{$single} = 1;
                push @finalstatement, $single;
                my @sields = split("\t",$single);
                $searchend = $sields[$endcord] + 1 if ($sields[$endcor
+d] + 1) > $searchend;
                $i = $sields[$startcord] - 2 if ($sields[$startcord] -
+ 1) < $searchstart;
                $searchstart = $sields[$startcord] - 1 if ($sields[$st
+artcord] - 1) < $searchstart;
            }
                        
        }
    }
    my $final = join("\t", @finalstatement)."\n";
    print ORTHS $final;
}

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In reply to Perl overwriting some lines by perlbrahmin

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