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# 1  
Old 09-26-2014
Perl error
New to perl, trying to decipher and fix the below error: Thanks.

Code:
 $ perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all -operation g,f -otherinfo”)' < file.txt
Can't find string terminator '"' anywhere before EOF at -e line 1.

# 2  
Old 09-26-2014
It is hard to debug program block structures from long one-liners.

I broke it down and it appears that the syntax of line 1 is correct - ' and " pairs exist.
The only missing character is the
Code:
system(.....);

at the end of the system() line.
# 3  
Old 09-26-2014
On top of that, you have edited your code in Microsoft Word -- which replaces all your normal " " quotes with nasty smart quotes.

Code:
perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all -operation g,f -otherinfo”)' < file.txt

Code:
perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all -operation g,f -otherinfo");' < file.txt

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