In the bash menu below if the variant that is inputted is in the format NM_004004.3:c.274G>T the below works perfectly. My question is if the variant inputted isNM_004004.3:-c.274G>T or NM_004004.3:+c.274G>T then the code as is will throw an error due to a biological issue. Is it possible to to have variants that have either a -/+ in them skip the additional function and go straight to the nomenclature function? I apologize for any confusion I am not sure how to explain this, but basically if variants with a -/+ in them go to the additional function then they will error. I don't know if there can be a special case coded in or if there is a better way. Thank you .
Code:
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/out.txt
done
add2text ${id}.txt
additional
}
Code:
nomenclature() {
# run python NameChecker
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
}
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LEARN ABOUT DEBIAN
explain_printf_or_die
explain_printf_or_die(3) Library Functions Manual explain_printf_or_die(3)NAME
explain_printf_or_die - formatted output conversion and report errors
SYNOPSIS
#include <libexplain/printf.h>
int explain_printf_or_die(const char *format);
int explain_printf_on_error(const char *format);
DESCRIPTION
The explain_printf_or_die function is used to call the printf(3) system call. On failure an explanation will be printed to stderr, obtained
from the explain_printf(3) function, and then the process terminates by calling exit(EXIT_FAILURE).
The explain_printf_on_error function is used to call the printf(3) system call. On failure an explanation will be printed to stderr,
obtained from the explain_printf(3) function, but still returns to the caller.
format The format, exactly as to be passed to the printf(3) system call.
RETURN VALUE
The explain_printf_or_die function only returns on success, see printf(3) for more information. On failure, prints an explanation and
exits, it does not return.
The explain_printf_on_error function always returns the value return by the wrapped printf(3) system call.
EXAMPLE
The explain_printf_or_die function is intended to be used in a fashion similar to the following example:
int result = explain_printf_or_die(format);
SEE ALSO printf(3)
formatted output conversion
explain_printf(3)
explain printf(3) errors
exit(2) terminate the calling process
COPYRIGHT
libexplain version 0.52
Copyright (C) 2010 Peter Miller
explain_printf_or_die(3)
10-27-2015
.