If the user inputs two variants separated by a comma, the below command is supposed to write both variants to the GJ-53.txt and then to out.txt. Both are written to the GJ-53.txt, however only one is written to out.txt and I'm not sure why. Thank you :).
gjb2() {
printf "\n\n"
printf "What is the id of the patient getting GJB2 analysis : "; read id
printf "Please enter the coding variant the following is an example"
echo " c.274G>T"
printf "variant(s), 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 "NM_004004.5:%s\n" ${variant[$i]} >> c:/Users/cmccabe/Desktop/Python27/$id.txt
done
add2text ${id}.txt
cd 'C:' C:/Users/cmccabe/Desktop/Python27/
printf "NM_004004.5:%s\n" "${variant}" >> c:/Users/cmccabe/Desktop/Python27/$id.txt >> c:/Users/cmccabe/Desktop/Python27/out.txt
additional
}
The set -x
+ cd 'C:\Users\cmccabe\Desktop\annovar'
+ echo -n ''
+ cd C: C:/Users/cmccabe/Desktop/Python27/
+ echo -n ''
+ menu
+ true
+ printf '\n Welcome to target gene annotation and mutalyzer (v1), please make a
selection from the MENU \n
==================================\n\n
\t 1 GJB2 analysis\n
\t 2 MECP2 analysis\n
\t 3 Phox2B analysis\n
\t 4 Syntax checker\n
\t 5 Name checker\n
\t 6 Position converter\n\n
==================================\n\n'
Welcome to target gene annotation and mutalyzer (v1), please make a selection f
rom the MENU
==================================
1 GJB2 analysis
2 MECP2 analysis
3 Phox2B analysis
4 Syntax checker
5 Name checker
6 Position converter
==================================
+ printf '\t Your choice: '
Your choice: + read menu_choice
1
+ case "$menu_choice" in
+ gjb2
+ printf '\n\n'
+ printf 'What is the id of the patient getting GJB2 analysis : '
What is the id of the patient getting GJB2 analysis : + read id
gj-53
+ printf 'Please enter the coding variant the following is an example'
Please enter the coding variant the following is an example+ echo ' c.274G>T'
c.274G>T
+ printf 'variant(s), use a comma between multiple: '
variant(s), use a comma between multiple: + IFS=,
+ read -a variant
c.109G>A,c.101T>C
+ '[' -z gj-53 ']'
+ '[' gj-53 = end ']'
+ (( i=0 ))
+ (( i<2 ))
+ printf 'NM_004004.5:%s\n' 'c.109G>A'
+ (( i++ ))
+ (( i<2 ))
+ printf 'NM_004004.5:%s\n' 'c.101T>C'
+ (( i++ ))
+ (( i<2 ))
+ add2text gj-53.txt
+ cd 'C:\Users\cmccabe\Desktop\annovar'
+ echo gj-53.txt
+ cd C: C:/Users/cmccabe/Desktop/Python27/
+ printf 'NM_004004.5:%s\n' 'c.109G>A'
+ additional
+ printf '\n\n'
+ printf 'Are there additonal target gene patients to be analyzed? Y/N '
Are there additonal target gene patients to be analyzed? Y/N + read match_choic
e
n
+ case "$match_choice" in
+ id=gj-53
+ nomenclature
+ printf '\n\n'
+ cd C:
+ C:/Users/cmccabe/Desktop/Python27/python.exe C:/Users/cmccabe/Desktop/Python27
/run_batch_job.py C:/Users/cmccabe/Desktop/Python27/out.txt C:/Users/cmccabe/Des
ktop/Python27/out_name.txt NameChecker
+ check
+ printf '\n\n'
