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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Kinshuk,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>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…<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>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.)<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Then you would run the script as perl duplicate.pl a.fsa >
unique.fsa<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>-Amir Karger<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
scriptome-users-bounces@bioinformatics.org
[mailto:scriptome-users-bounces@bioinformatics.org] <b>On Behalf Of </b>Kinshuk
Nayak<br>
<b>Sent:</b> Wednesday, February 11, 2009 3:37 AM<br>
<b>To:</b> scriptome-users@bioinformatics.org<br>
<b>Subject:</b> [Scriptome-users] help running Perl<o:p></o:p></span></p>
</div>
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<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal>Sir <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>I want to use script<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>perl -e '<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>$unique=0;<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>$total=0;<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>while(<>) {<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>if (/^>\S+/) {<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>$total++;<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>if (! ($seen{$&}++)) {<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>$unique++;<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>$print_it = 1<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>}<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>else {<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>$print_it = 0<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>}<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>};<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>if ($print_it) {<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>print $_<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>};<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>}<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>warn "\nChose $unique unique FASTA
records out of $total total.\n\n";<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>' a.fsa > unique.fsa<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>When i am saving the file and trying to run in perl
installed directory the message is<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>C:\NELU\PERL>duplicate.pl<br>
Bareword found where operator expected at C:\NELU\PERL\duplicate.pl line 21,
nea<br>
r "' a"<br>
(Might be a runaway multi-line '' string starting on line 1)<br>
(Missing operator before a?)<br>
syntax error at C:\NELU\PERL\duplicate.pl line 1, near "perl -e "<br>
Execution of C:\NELU\PERL\duplicate.pl aborted due to compilation errors.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN>C:\NELU\PERL><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span lang=EN> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><span lang=EN>Could you
please suggest me some ways to solve it</span><o:p></o:p></p>
</div>
<p class=MsoNormal>Kinshuk Chandra Nayak <o:p></o:p></p>
</td>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
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style='font-size:10.0pt;font-family:"Calibri","sans-serif"'>
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