in reply to Re^2: How can I print all lines?
in thread How can I print all lines?

That's because you only print once, at the end. Move the print inside the while loop if you want to print each line as it is processed.

Thanks for adding the <code> tags, but now your code is littered with <p> tags, etc. Can you remove those? It will make it much easier for us to read and understand. Update: thanks for sorting that.

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Re^4: How can I print all lines?
by 345qwerty (Novice) on Aug 10, 2017 at 11:52 UTC

    I changed my code a bit, but now it prints in this way:

    5 Q CAA OUT16 Q CAG OUT

    21 Q CAA OUT

    74 Q CAA OUT

    80 Q CAG OUT

    82 Q CAG OUT

    84 Q CAG OUT

    85 Q CAG OUT

    89 Q CAG

    IN

    90 Q CAG

    IN

    91 Q CAG

    IN

    92 Q CAG

    IN

    93 Q CAA

    IN

    94 Q CAG

    IN

    95 Q CAG

    IN

    96 Q CAG

    IN

    98 Q CAG OUT

    99 Q CAG OUT

    100 Q CAG OUT

    I would like to get:

    My OUTPUT FILE:

    5 Q CAA OUT

    16 Q CAG OUT

    21 Q CAA OUT

    74 Q CAA OUT

    80 Q CAG OUT

    82 Q CAG OUT

    84 Q CAG OUT

    85 Q CAG OUT

    89 Q CAG IN

    90 Q CAG IN

    91 Q CAG IN

    92 Q CAG IN

    93 Q CAA IN

    94 Q CAG IN

    95 Q CAG IN

    96 Q CAG IN

    98 Q CAG OUT

    99 Q CAG OUT

    100 Q CAG OUT

    Here is my code: 

    use strict; 
use warnings;

open(FILE, "<", "Q.txt");

my @column=(<FILE>);    #get the lines from the standard input into an
+ array
my $file;
chomp $file;                 
    my $number=0;
        while($number <= $#column) {       #go through the array from 
+0 to the last element
         my $j;
         my $count=0;
              foreach ($j=$number; $j < $#column; $j++) {    #select t
+he numbers from the beginning of the line in the current and next ele
+ment
    
                my $d=($column[$j]=~/(\d+)/)[0] - ($column[$j+1]=~/(\d
++)/)[0]; #difference
                last if abs($d)!= 1;       #if differ more than 1 - le
+ave  
     
                 $count+=$d;       #accumulate the difference
  
    }     
             if(abs($count)>=7) {
             chomp($column[$_]);
               $column[$_]=$column[$_]. "\tIN\n" for $number..$j;     
+  #IN if >8
              $number=$j+1;  
             } 
                if (abs($count)<8) {
                chomp($column[$number]);
                   $column[$number] = $column[$number]."\tOUT\n";     
+  #OUT if < 8
                   $number++;
                 }
    }

print for @column;

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[d/l]

      Step 1: What exactly is it you don't like? (CRLF in the middle of your print)

      Step 2: Where in the code does it do that? (Somewhere between printing the text of the line and printing the IN or OUT, conveniently, this is on the same line so you don't have to look very far.)

      Step 3: Consider what it is doing there. Add debug prints to make clear what your variables are at that point. (There's a \n before your \tIN... and the $column[$number] is the thing before the \t... print "-=)$column[$number](=-";? Well, that will prove that you've got a CRLF in there.)

      Step 4: Understand. The CRLF is in your string because every line of your file ends with a CRLF, of course!

      Step 5: Fix it. chomp was made for this.

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