• What did you try? (Code)
• How did it fail? (Details, error message)
• We try to help you learn. (This is not code-a-matic)
• Read the markup instructions around the text-entry box. (<p>...</p> and <c>...</c> or even Markup in the Monastery!)

Or a variation of the above solution:

use Modern::Perl;

my %hash;

do {chomp; $_ = qq|$_"$hash{$1}"| if /(ID=.+)$/ and ++$hash{$1}; say}
  for <DATA>;

__DATA__
xxxx . yyy 521 916 . + . ID=OSCAR1028v1rpkm9.67

xxxx . xxx 521 567 . + . Parent=OSCAR1028v1rpkm9.67

xxxx . yyy 126 130 . - . ID=OSCAR10281vrpkm9.67

xxxx . xxx 129 130 . - . Parent=OSCAR1028v1rpkm9.67

xxxx . yyy 126 130 . - . ID=OSCAR10281vrpkm9.67

xxxx . xxx 129 130 . - . Parent=OSCAR1028v1rpkm9.67
[download]

Results:

xxxx . yyy 521 916 . + . ID=OSCAR1028v1rpkm9.67"1"

xxxx . xxx 521 567 . + . Parent=OSCAR1028v1rpkm9.67

xxxx . yyy 126 130 . - . ID=OSCAR10281vrpkm9.67"1"

xxxx . xxx 129 130 . - . Parent=OSCAR1028v1rpkm9.67

xxxx . yyy 126 130 . - . ID=OSCAR10281vrpkm9.67"2"

xxxx . xxx 129 130 . - . Parent=OSCAR1028v1rpkm9.67
[download]

this is what I want but without double quote surrounding the number.

but I say in my last mail I am a very scarce in

programming and I written this script to use your code

but I can able to do correctly where is my mistake.

My data are in txt file so I make this script to read

them. <code> #!/usr/bin/perl; use strict; use warnings; use Modern::Perl; my $filename = $ARGV[0]; my $debug = $ARGV1; die "\n\tUSAGE: perl $0 exonerate output debug\n\n" unless $ARGV[0]; die "\n\tERROR: Cannot find the file $ARGV[0]\n\n" unless -e $ARGV[0]; open(IN,$filename); my $ids; my %hash; do {chomp; $_ = qq|$_"$hash{$1}"| if /(ID=.+)$/ and ++$hash{$1}; say} for $filename;

but I have a error " Cant locate Modern::Perl .."

I suppose that I don't have this module have you

suggestion to resolve it. If I want to use the code by monsoon <code> while(<>){ chomp; if(/(ID=.+)$/){ if(++$ids{$1} > 1){ say $_, $ids{$1}; next; } } say; }

its good to insert it in my script in this way <code> #!/usr/bin/perl; use strict; use warnings; my $filename = $ARGV[0]; my $debug = $ARGV1; die "\n\tUSAGE: perl $0 exonerate output debug\n\n" unless $ARGV[0]; die "\n\tERROR: Cannot find the file $ARGV[0]\n\n" unless -e $ARGV[0]; open(IN,$filename); my $ids; while($filename){ chomp; if(/(ID=.+)$/){ if(++$ids{$1} > 1){ say $_, $ids{$1}; next; } } say; } print say;

Hi, blacknight.

In case the Modern::Perl error is still occurring, try the following to produce the results you wanted w/o "quotes":

use strict;
use warnings;

my %hash;

do { chomp; $_ = qq|$_.$hash{$1}| if /(ID=.+)$/ and ++$hash{$1}; print
+ "$_\n" }
  for <DATA>;
[download]

You mean something like this?

while(<>){
    chomp;
    if(/(ID=.+)$/){
        if(++$ids{$1} > 1){ 
            say $_, $ids{$1};
            next;
        }        
    }
    say;    
}
[download]

Try and get yourself a copy of the Perl Cookbook. It usually comes handy for such tasks.

#!/usr/bin/perl; use strict; use warnings; my $filename = $ARGV[0]; my $debug = $ARGV1; die "\n\tUSAGE: perl $0 output debug\n\n" unless $ARGV[0]; die "\n\tERROR: Cannot find the file $ARGV[0]\n\n" unless -e $ARGV[0]; open(IN,$filename); my $ids; while($filename){ chomp; if(/(ID=.+)$/){ if(++$ids{$1} > 1){ say $_, $ids{$1}; next; } } say; } print say;

I am sorry for my english and my script error

see you

Continuing with the issues and advice:

Please surround your code and data listings with <c> (at the beginning) and </c> (at the end). It makes your nodes much easier to read, and thus, more likely to draw help.

Your indentation style may have been different, but surely you saw that your code didn't look 'right' (for some value of 'right' meaning 'easy to read'):

#!/usr/bin/perl; 
use strict; 
use warnings; 
my $filename = $ARGV[0]; 
my $debug = $ARGV1; 
die "\n\tUSAGE: perl $0 output debug\n\n" unless $ARGV[0]; 
die "\n\tERROR: Cannot find the file $ARGV[0]\n\n" unless -e $ARGV[0];
+ 
open(IN,$filename); 
my $ids; 
while($filename){ 
    chomp; 
    if(/(ID=.+)$/){ 
        if(++$ids{$1} > 1){ 
            say $_, $ids{$1}; 
            next; 
        } 
    } 
    say; 
} 
print say;
[download]

The say in Line 18 probably doesn't do what you intended; print say; in Line 20 is meaningless.

say is "Just like "print", but implicitly appends a newline" to quote the 5.014 doc. To use it, either include use 5.010 (or higher; 5.016 is current) as monsoon suggested or use feature qw(switch say); (where feature is a (relatively new) pragma to enable new features that are not available without specifically enabling them).

Other issues start with the unnecessary (but harmless) semi-colon at the end of the hashbang (or, in order of severity, your incorrect attempt to invoke debug mode, as noted by monsoon.

It would help if your code was properly formatted. Anyway, to use 'say' you need to

use v5.10;
[download]

for "my $debug" declaration you probably meant

my $debug = $ARGV[1];
[download]

'ids' need to be declared as a hash, not a scalar

my %ids;
[download]

while loop needs to read from the file handle that you opened instead of checking the truth value of $filename variable which causes infinite loop if $filename is anything other than 0 or empty string

while(<IN>)
[download]

'print say' at the end doesn't really do any good