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

Amir Karger akarger at CGR.Harvard.edu
Thu Jun 4 12:24:29 EDT 2009



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



I want to use script

perl -e '



while(<>) {

if (/^>\S+/) {


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


$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


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.




Could you please suggest me some ways to solve it

Kinshuk Chandra Nayak 



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