[Scriptome-users] Saving Scriptome tool as an executable script (was RE: help running Perl)

[Amir Karger]

Kinshuk,

 

I’m sorry it took several months to find this email. You need to subscribe to the list to send emails to it, or it goes into a spam folder.  Anyway, if it will still be of use…

 

If you want to save the Perl as an executable script, you need to get rid of the first line (perl -e ‘) and the last line (‘a.fsa  etc.)

Then you would run the script as perl duplicate.pl a.fsa > unique.fsa

 

-Amir Karger

 

From: scriptome-users-bounces at bioinformatics.org [mailto:scriptome-users-bounces at bioinformatics.org] On Behalf Of Kinshuk Nayak
Sent: Wednesday, February 11, 2009 3:37 AM
To: scriptome-users at bioinformatics.org
Subject: [Scriptome-users] help running Perl

 

Sir 

I want to use script

perl -e '

$unique=0;

$total=0;

while(<>) {

if (/^>\S+/) {

$total++;

if (! ($seen{$&}++)) {

$unique++;

$print_it = 1

}

else {

$print_it = 0

}

};

if ($print_it) {

print $_

};

}

warn "\nChose $unique unique FASTA records out of $total total.\n\n";

' a.fsa > unique.fsa

 

 

When i am saving the file and trying to run in perl installed directory the message is

 

C:\NELU\PERL>duplicate.pl
Bareword found where operator expected at C:\NELU\PERL\duplicate.pl line 21, nea
r "' a"
  (Might be a runaway multi-line '' string starting on line 1)
        (Missing operator before a?)
syntax error at C:\NELU\PERL\duplicate.pl line 1, near "perl -e "
Execution of C:\NELU\PERL\duplicate.pl aborted due to compilation errors.

C:\NELU\PERL>

 

 

Could you please suggest me some ways to solve it

Kinshuk Chandra Nayak 

 

________________________________

Connect with friends all over the world. Get Yahoo! India Messenger. <http://in.rd.yahoo.com/tagline_messenger_1/*http:/in.messenger.yahoo..com/?wm=n/> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/scriptome-users/attachments/20090604/836e8a58/attachment.html>