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Bash menu opens and closes
03-11-2015
. additional() {
printf "\n\n"
printf "Are there additonal GJB2 patients to be analyzed? Y/N "; read match_choice
case "$match_choice" in
[yY]) id=""; gjb2 ;;
[nN]) id=""; annovar ;;
esac
}
annovar() {
printf "\n\n"
printf "How many patients : "; read id
[ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
[ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu
cd 'C:\Users\cmccabe\Desktop\annovar'
$( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < sanger.txt )
printf "The annotation is complete, would you like analyze additional patients : "; read match_choice
case "$match_choice" in
[yY]) id=""; menu ;;
[nN]) id=""; printf "\n Goodbye! \n\n"; exit ;;
}
# actual start of this program
menu # run menu function
03-11-2015
03-12-2015
, it is working now... # run python NameChecker
cd 'C:'
C:/Users/cmccabe/Desktop/Python27/python.exe C:/Users/cmccabe/Desktop/Python27/run_batch_job.py C:/Users/cmccabe/Desktop/Python27/${id}.txt NameChecker
check() {
printf "\n\n"
printf "Is the variant correct? Y/N "; read match_choice
case "$match_choice" in
[yY]) id=""; position ;;
[nN]) id=""; gjb2 ;; echo -n "" > ${id}.txt
esac
}
position() {
# run python PositionConverter
printf "\n\n"
cd 'C:'
C:/Users/cmccabe/Desktop/Python27/python.exe C:/Users/cmccabe/Desktop/Python27/run_batch_job.py C:/Users/cmccabe/Desktop/Python27/${id}.txt C:/Users/cmccabe/Desktop/annovar/${id}.txt PositionConverter
convert
}
03-12-2015
. gjb2() {
printf "\n\n"
printf "What is the id of the patient getting GJB2 analysis : "; read id
printf "Enter variant: "; read variant
[ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && return
[ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && return
# save file in windows python directory
printf "%s\n" "$variant" > c:/Users/cmccabe/Desktop/Python27/$id.txt
# add transcript
sed -i '$a NM_004004.5:' c:/Users/cmccabe/Desktop/Python27/$id.txt
printf "NM_004004.5:%s\n" "$variant" > c:/Users/cmccabe/Desktop/Python27/$id.txt
03-12-2015
.menu -> gjb2 -> name -> check -> position -> parse -> add2text -> additional? -> annovar -> menu or message and exit
^ ^
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user mecp2 -> name -> check -> position -> parse -> add2text -> additional? -> annovar -> menu or message and exit
choice ^
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phox2b -> name -> check -> position -> parse -> add2text -> additional? -> annovar -> menu or message and exit
^
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+----------------------------------------------------------------------------------------------------------+
^
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exitmenu choice - user is prompted for selection (4 choices)
selection - each selection has unique transcript assigned
name - python script to verify name syntax
check - user prompted to verify naming correct (Y/N) - after python script is run results of that appear on screen, so that the prompt can be answered
if the answer is "Y" then next function (position), if "n" then return to function gjb2 and ${id}.txt cleared
position - python script to transfer ${id}.txt to annovar directory and convert to coordinates
parse - parse specific field to create ${id}_parse.txt
add2text - ${id}.txt is added to sanger.txt
additional - user is asked for additional data (Y/N) - if "Y" then goto to gjb2 function, if "N" then goto annovar function
annovar - perl script run on ${id}_parse.txt
after the script is run the user is told its completed and asked if there is more to do(Y/N) - if "Y" then menu function, if "N" then message and exit|
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