RE: string substitution command question

2011-02-26 Thread Katya Gorodinsky
, 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

Re: string substitution command question

2011-02-26 Thread Richard Green
Ok JD thanks On Feb 26, 2011, at 3:46 PM, John Delacour wrote: > At 12:57 -0800 26/02/2011, Richard Green wrote: > > >> > What is $gene_id? >>> Are you by any chance using '$' at the beginning of your search pattern >>> instead of the end? >> I have $ to designate the end of the row >> $

Re: string substitution command question

2011-02-26 Thread John Delacour
At 12:57 -0800 26/02/2011, Richard Green wrote: > What is $gene_id? Are you by any chance using '$' at the beginning of your search pattern instead of the end? I have $ to designate the end of the row $gene_id $gene_id designates $gene_id period. > Why are you escaping the quote marks?

Re: string substitution command question

2011-02-26 Thread Parag Kalra
On Sat, Feb 26, 2011 at 12:56 PM, Uri Guttman wrote: > > "PK" == Parag Kalra writes: > > >> why are you doing s/// against $_? by default it does that. > > you didn't rectify this one. > Oops. Missed that. > > > PK> Sorry. Hope this reply is better and so as the following code: > > muc

Re: string substitution command question

2011-02-26 Thread Richard Green
> What is $gene_id? > Are you by any chance using '$' at the beginning of your search pattern > instead of the end? I have $ to designate the end of the row $gene_id > > Why are you escaping the quote marks? I thought it would be easier to perform substitution without them > > Why is there n

Re: string substitution command question

2011-02-26 Thread Uri Guttman
> "PK" == Parag Kalra writes: >> why are you doing s/// against $_? by default it does that. you didn't rectify this one. PK> Sorry. Hope this reply is better and so as the following code: much better. PK> use strict; PK> use warnings; PK> while(){ PK> $_ =~ s/NM_(\d+

Re: string substitution command question

2011-02-26 Thread Uri Guttman
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Re: string substitution command question

2011-02-26 Thread Parag Kalra
On Sat, Feb 26, 2011 at 12:34 PM, Uri Guttman wrote: > > "PK" == Parag Kalra writes: > > PK> use strict; > PK> use warnings; > PK> while(){ > PK> chomp; > > why are you chomping here when you add in the \n later? > Agreed and corrected in the example at the bottom. > PK> if

Re: string substitution command question

2011-02-26 Thread Uri Guttman
> "PK" == Parag Kalra writes: PK> use strict; PK> use warnings; PK> while(){ PK> chomp; why are you chomping here when you add in the \n later? PK> if ($_ =~ /NM_(\d+)/){ PK> my $found = $1; PK> $_ =~ s/$found/$found:12345/g; many issues there. why do

Re: string substitution command question

2011-02-26 Thread John Delacour
At 12:06 -0800 26/02/2011, Richard Green wrote: chr1ucscexon226488874 226488906 0.00 - . gene_id "NM_173083:12345"; transcript_id "NM_173083:12345"; chr1ucscexon226496810 226497198 0.00 - . gene_id "NM_173083:12345";

Re: string substitution command question

2011-02-26 Thread Parag Kalra
use strict; use warnings; while(){ chomp; if ($_ =~ /NM_(\d+)/){ my $found = $1; $_ =~ s/$found/$found:12345/g; print "$_\n"; } else { print "$_\n"; } } __DATA__ chr1ucscexon226488874 226488906 0.00 - . gene_id

string substitution command question

2011-02-26 Thread Richard Green
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: chr1ucscexon226488874 226488906 0.00 - . gene_id "NM_173083"; transcript_id "NM_173083"; chr1