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2 shells in one file
10-29-2014
printf "Is this a batch or sanger analysis :" ; read id
. #!/bin/bash
while true
do
printf "Does the file need to be converted : " ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
case "$id" in
[yY]) perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput
;;
[nN]) # code for X
Goto line 14
done
while true
do
printf "Is this a batch or sanger analysis :" ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
case "$id" in
[yY]) perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt
;;
[nN]) # code for X
printf "Enter ID : " ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
[ -z "$id" ] && break
[ "$id" = "end" ] && break
perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo
;;
end) break ;;
*) ;; # Unknown option, do nothing
esac
Goto line 4
done
10-29-2014
10-29-2014
#!/bin/bash
while true
do
printf "Enter ID : " ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
[ -z "$id" ] && break
[ "$id" = "end" ] && break
perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput
done #!/bin/bash
while true
do
printf "Is this a batch or sanger analysis :" ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
case "$id" in
[yY]) perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt
;;
[nN]) # code for X
printf "Enter ID : " ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
[ -z "$id" ] && break
[ "$id" = "end" ] && break
perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo
;;
end) break ;;
*) ;; # Unknown option, do nothing
esac
printf "Is this a batch or sanger analysis :"
done #!/bin/bash
while true
do
printf "Enter ID : " ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
[ -z "$id" ] && break
[ "$id" = "end" ] && break
perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput
done #!/bin/bash
while true
do
printf "Is this a batch or sanger analysis :" ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
case "$id" in
[yY]) perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt
;;
[nN]) # code for X
printf "Enter ID : " ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
[ -z "$id" ] && break
[ "$id" = "end" ] && break
perl table_annovar.pl ${id}_matched.avinput humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo
;;
end) break ;;
*) ;; # Unknown option, do nothing
esac
printf "Is this a batch or sanger analysis :"
done perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput.
10-31-2014
Thanks.|
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