Hi,
What about this solution:
use warnings;
use strict;
my $str = ' chr1 ucsc exon 226488874 226488906 0.000000
- . gene_id "NM_173083"; transcript_id "NM_173083";
chr1 ucsc exon 226496810 226497198 0.000000
- . gene_id "NM_173083"; transcript_id "NM_173083";
chr1 ucsc exon 2005086 2005368 0.000000 + .
gene_id "NM_001033581"; transcript_id "NM_001033581";
chr1 ucsc exon 2066701 2066786 0.000000 + .
gene_id "NM_001033581"; transcript_id "NM_001033581";';
my @patterns = map {/(NM_\d+)"/; $1} grep(/NM_\d+"/, split(/\n+/, $str));
my $additional = 12345;
foreach (@patterns) {
$str =~ s/($_)\"/$1:$additional\"/g and $additional++;
}
print "$str\n";
Regards,
Katya
-----Original Message-----
From: Richard Green [mailto:gree...@uw.edu]
Sent: Saturday, February 26, 2011 10:07 PM
To: beginners@perl.org
Subject: string substitution command question
Hi Perl users, Quick question, I have a one long string with tab delimited
values separated by a newline character (in rows)
Here is a snippet of the the string:
chr1 ucsc exon 226488874 226488906 0.000000
- . gene_id "NM_173083"; transcript_id "NM_173083";
chr1 ucsc exon 226496810 226497198 0.000000
- . gene_id "NM_173083"; transcript_id "NM_173083";
chr1 ucsc exon 2005086 2005368 0.000000 + .
gene_id "NM_001033581"; transcript_id "NM_001033581";
chr1 ucsc exon 2066701 2066786 0.000000 + .
gene_id "NM_001033581"; transcript_id "NM_001033581";
I am trying to perform substitution on some values at the end of each rows,
for example, I'm trying to replace the above string with the following:
chr1 ucsc exon 226488874 226488906 0.000000
- . gene_id "NM_173083:12345"; transcript_id "NM_173083:12345";
chr1 ucsc exon 226496810 226497198 0.000000
- . gene_id "NM_173083:12345"; transcript_id "NM_173083:12345";
chr1 ucsc exon 2005086 2005368 0.000000 + .
gene_id "NM_001033581:12346"; transcript_id "NM_001033581:12346";
chr1 ucsc exon 2066701 2066786 0.000000 + .
gene_id "NM_001033581:12346"; transcript_id "NM_001033581:12346";
Here is the substitution command I am trying to use:
$data_string=~ s/$gene_id\"NM_173083\"\; transcript_id
\"NM_173083\"\;/\"NM_173083:12345\"\; \"NM_173083:12345\"\;/g;
$data_string=~ s/$gene_id\"NM_001033581\"\; transcript_id
\"NM_001033581\"\;/\"NM_001033581:12346\"\; \"NM_001033581:12346\"\;/g;
I don't know why I am not able to substitute at the end of each row in the
string.
Any suggestions folks have are muchly appreciated. Thanks -Rich
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