in reply to Re^2: rename duplicate data
in thread rename duplicate data

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>;

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Re^4: rename duplicate data
by Anonymous Monk on Jun 24, 2012 at 20:36 UTC

    Hi Kenosis

    I tanks you very much.

    You are fantastic.

    the output its right, as I want it, but now I have the numbering also in non duplicate ID

    .... ID=Locus10035v1rpkm10.18.1

    .... Parent=Locus10035v1rpkm10.18

    .... ID=Locus10035v2rpkm2.50.1

    .... Parent=Locus10035v2rpkm2.50

    .... ID=Locus10073v1rpkm10.09.1

    .... Parent=Locus10073v1rpkm10.09

    .... ID=Locus10182v1rpkm9.88.1

    .... Parent=Locus10182v1rpkm9.88

    .... ID=Locus10210v1rpkm9.81.1

    but I would like to have only on duplicate and the numbering start only from second and so on.

[reply]
Re^4: rename duplicate data
by blacknight (Initiate) on Jun 26, 2012 at 11:11 UTC

    Hi everyone I tried to resolve my issue on renaming duplicate data whit this script. But It don't obtain a result. where is my mistake? My aims is to obtain this format Parent same name of its previous ID, this is a imput file

    0409 . mR 21213 23782 12787 + . ID=0035v110.18"1" 0409 . ex 21213 23782 . + . Parent=0035v110.18 0409 . mR 22173 24122 9669 - . ID=0035v22.50"1" 0409 . ex 22173 24122 . - . Parent=0035v22.50 0409 . mR 86435 89419 14907 - . ID=0073v110.09"1" 0409 . ex 86435 89419 . - . Parent=0073v110.09 0409 . mR 76753 78963 10984 + . ID=0182v19.88"1" 0409 . ex 76753 78963 . + . Parent=0182v19.88 0409 . mR 40542 45144 20377 - . ID=0210v19.81"1" 0409 . ex 45014 45144 . - . Parent=0210v19.81 0409 . ex 44717 44939 . - . Parent=0210v19.81 0409 . ex 44592 44625 . - . Parent=0210v19.81 0409 . ex 41343 44469 . - . Parent=0210v19.81 0409 . ex 41205 41221 . - . Parent=0210v19.81 0409 . ex 40542 41122 . - . Parent=0210v19.81 0409 . mR 43128 45064 8216 + . ID=0210v20.31_PRE"1" 0409 . ex 43128 44469 . + . Parent=0210v20.31_PRE 0409 . ex 44592 44625 . + . Parent=0210v20.31_PRE 0409 . ex 44717 44939 . + . Parent=0210v20.31_PRE 0409 . ex 45014 45064 . + . Parent=0210v20.31_PRE

    <code> use warnings; use feature "say"; use Data::Dumper; 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 $row = <IN>; my @tabula; my $i = 0; while ($row = <IN>) { $i++; @tabula = "$i) $row"; my $row = split(/\n/,@tabula); my @new_tabula = split(/\t/,$row); #print @tabula; my @field = @tabula; foreach (my @field) { my $id; my $string; if($field2 eq 'mR') { $field8 =~ /\tID(=.+)'$/; $id = $1; $string = "$field[0]\t.\tmR\t$field3\t$field4\t$field5\t$field6\t$field7\tID=$id\n"; } elsif($field2 eq 'ex') { $string = "$field[0]\t.\tex\t$field3\t$field4\t$field5\t$field6\t$field7\tParent=$id\n"; } print $string if $string; } } <code>

[reply]

      Hi blacknight,

      I see from your post’s HTML source that you have made an effort at correct formatting. Unfortunately, you made three mistakes:

      • The input file needs to be formatted as code. Replace the outer <p> and </p> with <code> and </code>.
      • For your script, you have written &lt;code> where you need to use a literal < character: <code>.
      • Your closing </code> tag is missing the slash ‘/’ character.

      Please make these changes and re-submit using the ‘update’ button. This will make it much easier for the monks to help you.

      Regards,

      Athanasius <°(((>< contra mundum

[reply]

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