I have the below bash
which runs great. Before I make a change I wanted to check with experts (as I am not one). After the perl
code completes, I am going to display "annotation complete" then go into the remove function
.
annovar() {
# combine id and position files
cd 'C:\Users\cmccabe\Desktop\annovar'
cp out_parse.txt "$(cat target.txt)"
# run annotation
$( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f ")' < target.txt )
printf "The annotation is complete, would you like analyze additional target gene patients? Y/N "; read match_choice
case "$match_choice" in
[yY]) id="${id}"; menu ;;
[nN]) id="${id}"; remove ;;
esac
}
My question is will something like this work: Thank you :).
annovar() {
# combine id and position files
cd 'C:\Users\cmccabe\Desktop\annovar'
cp out_parse.txt "$(cat target.txt)"
# run annotation
$( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f ")' < target.txt )
printf "The annotation is complete "; remove
esac
}