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Bash function to suppress warning message for specific text and display prompt
03-07-2017
# enter variant
phox2b() {
printf "\n\n"
printf "What is the id of the patient getting Phox2B analysis : "; read id
printf "Please enter the coding variant the following is an example"
echo " c.274G>T or c.274-10G>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_003924.3:%s\n" ${variant[$i]} >> c:/Users/cmccabe/Desktop/Python27/out.txt
done
add2text ${id}.txt
additionalNM_003924.3:c.242-1G>A NM_003924.3:c.*18_*19delGCinsAA NM_003924.3:c.013G>T NM_003924.3:c.013C>T
# run python NameChecker
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/Desktop/Python27/out_name.txt NameChecker
check
}
# verify
check() {
printf "\n\n"
awk 'NR>1 { if ($2 ~ /^\(/ ) {$1=""; print "Found error: ", $0} else { sub(/.*:/, "", $1); sub(/.*:/, "", $7); print "No error: " $1 "," $7}}' C:/Users/cmccabe/Desktop/Python27/out_name.txt
printf "Is the variant correct? Y/N "; read match_choice
case "$match_choice" in
[yY]) id="${id}"; convert ;;
[nN]) cd 'C:' C:/Users/cmccabe/Desktop/Python27/; awk '/variantchecker/ {r[$1]} FNR==NR {next} !($1 in r)' c:/Users/cmccabe/Desktop/Python27/out_name.txt c:/Users/cmccabe/Desktop/Python27/out.txt > c:/Users/cmccabe/Desktop/Python27/out.txt; rm c:/Users/cmccabe/Desktop/Python27/out_name.txt; menu ;;
esac
}
# run python PositionConverter
convert() {
printf "\n\n"
cd 'C:'
C:/Users/cmccabe/Desktop/Python27/python.exe C:/Users/cmccabe/Desktop/Python27/run_batch_job.py C:/Users/cmccabe/Desktop/Python27/out.txt C:/Users/cmccabe/Desktop/annovar/out_position.txt PositionConverter
parse
}Input Errors and warnings AccNo Genesymbol Variant Reference Sequence Start Descr. Coding DNA Descr. Protein Descr. GeneSymbol Coding DNA Descr. GeneSymbol Protein Descr. Genomic Reference Coding Reference Protein Reference Affected Transcripts Affected Proteins Restriction Sites Created Restriction Sites Deleted NM_003924.3:c.242-1G>A (variantchecker): Intronic position given for a non-genomic reference sequence. NM_003924.3:c.*18_*19delGCinsAA NM_003924.3 PHOX2B_v001 c.*18_*19delGCinsAA n.1323_1324delinsAA c.*18_*19delinsAA p.(=) PHOX2B_v001:c.*18_*19delinsAA PHOX2B_v001:p.(=) NM_003924.3 NP_003915.2 NM_003924.3(PHOX2B_v001):c.*18_*19delinsAA NM_003924.3(PHOX2B_i001):p.(=) HpyAV NM_003924.3:c.013G>T NM_003924.3 PHOX2B_v001 c.013G>T n.373G>T c.13G>T p.(Glu5*) PHOX2B_v001:c.13G>T PHOX2B_v001:p.(Glu5*) NM_003924.3 NP_003915.2 NM_003924.3(PHOX2B_v001):c.13G>T NM_003924.3(PHOX2B_i001):p.(Glu5*) NM_003924.3:c.013C>T (variantchecker): C not found at position 373, found G instead.
.# enter variant
phox2b() {
printf "\n\n"
printf "What is the id of the patient getting Phox2B analysis : "; read id
printf "Please enter the coding variant the following is an example"
echo " c.274G>T or c.274-10G>T"
printf "variant(s), use a comma between multiple: "; IFS="," read -a variant
[ -z "$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_003924.3:%s\n" ${variant[$i]} >> c:/Users/cmccabe/Desktop/Python27/out.txt
done
add2text ${id}.txt
additional
# run python NameChecker
nomenclature() {
printf "\n\n"
cd 'C:'
C:/Users/cmccabe/Desktop/Python27/python.exe C:/Users/cmccabe/Desktop/Python27/run_batch_job.py C:/Users/cmccabe/Desktop/Python27/out.txt C:/Users/cmccabe/Desktop/Python27/out_name.txt NameChecker
# read each variant that matches patterern into LINE
while read LINE; do
grep -oP '[ "$variant" == "${variant#*[+-]}" ]\K.*'
done < c:/Users/cmccabe/Desktop/Python27/out.txt
# supress warning message and display message
grep -q '(variantchecker): Intronic position given for a non-genomic reference sequence.' 'C:/Users/cmccabe/Desktop/Python27/out_name.txt' || echo "$LINE is an intronic variant";
check
}
# verify
check() {
printf "\n\n"
awk 'NR>1 { if ($2 ~ /^\(/ ) {$1=""; print "Found error: ", $0} else { sub(/.*:/, "", $1); sub(/.*:/, "", $7); print "No error: " $1 "," $7}}' C:/Users/cmccabe/Desktop/Python27/out_name.txt
printf "Is the variant correct? Y/N "; read match_choice
case "$match_choice" in
[yY]) id="${id}"; convert ;;
[nN]) cd 'C:' C:/Users/cmccabe/Desktop/Python27/; awk '/variantchecker/ {r[$1]} FNR==NR {next} !($1 in r)' c:/Users/cmccabe/Desktop/Python27/out_name.txt c:/Users/cmccabe/Desktop/Python27/out.txt > c:/Users/cmccabe/Desktop/Python27/out.txt; rm c:/Users/cmccabe/Desktop/Python27/out_name.txt; menu ;;
esac
}
# run python PositionConverter
convert() {
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/Desktop/annovar/out_position.txt PositionConverter
parse
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