The below bash function uses multiple variables CODING, SAMPLE, SURVEY, andvariant
in it. The user selects the cap function and details are displayed on the screen using the $SURVEY variable, the directory is changed to $SAMPLE and the samples.txt is opened so the user can select the sample to use. The numeric id is entered along with some $variant (could be multiple) and the $CODING:$variant are written to an out.txt file and stored /home/cmccabe/cap/TGS. I am getting a syntax error on the last line looking for the matching ' and am not sure if I am using the variables correctly in the function. Thank you .
samples.txt in $SAMPLE
Code:
test-01
test-02
test-03
test-04
$SURVEY format
Code:
Survey id
name
details
$CODING format
Code:
NM_000012.3
Code:
cap() {
CODING=/home/cmccabe/cap/TGS/NM.txt
SAMPLE=/home/cmccabe/cap/TGS
SURVEY=/home/cmccabe/cap/TGS
printf "The survey being used is and here are the details:" "$SURVEY\survey.txt "
PS3="please select a file to analyze with a panel: "
cd "$SAMPLE"
select file1 in $(cat samples.txt)
do [ "$file1" != "" ] && break
done
printf "FILE is: ${file1} and will be used for annotation\n"
read -r -p "Is this correct? [y/N] " response
if [[ $response =~ ^[nN][oO]?$ ]]
then
echo 'please try again' && return
printf "\n\n"
printf "What is the id of the CAP sample getting gene annotation : "; read id
printf "Please enter the variant(s), the following are examples"
echo " c.274G>T or c.274-10G>T or c.*18_*19delGCinsAA"
printf "and please use a comma between multiple: "; IFS="," read -a variant
[ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && return
[ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && return
for ((i=0; i<${#variant[@]}; i++))
do printf ${CODING}:%s\n ${variant[$i]} >> /home/cmccabe/cap/TGS/out.txt
done
}
Last edited by cmccabe; 03-23-2017 at 01:39 PM..
Reason: fixed format and added details
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03-23-2017
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