Combine shell files

Shell Programming and Scripting
1

The script below is an attempt to combine 3 shells into 1.

The first part: match.sh
prompts the user for an id of a patient and runs a match script based on the response of "y" or "n". After completing the user is asked if there are additional patients, and based on "y" or "n" a certain action is followed.

The second part: convert2annovar.sh
prompts the user for an id of a patient and runs a conversion script based on the response of "y" or "n". After completing the user is asked if there are additional patients, and based on "y" or "n" a certain action is followed.

The third part: table_annovar
prompts the user for the type of analysis and runs a script based on the response of "y" or "n". After completing the user is asked if there are additional patients, and based on "y" or "n" a certain action is followed.

I attached the .sh file as well. Thank you :).

2

Question, does this run for you as expected?

+ ~ $ sh annovar.sh 
What is the id of the patient to be matched  : 3
': not a valid identifier `id
What panel: 3
': not a valid identifier `panel
annovar.sh: line 4: syntax error near unexpected token `$'in\r''
'nnovar.sh: line 4: `		case "$id" in

2 ~ $ sh annovar.sh 
What is the id of the patient to be matched  : a
': not a valid identifier `id
What panel: b
': not a valid identifier `panel
annovar.sh: line 4: syntax error near unexpected token `$'in\r''
'nnovar.sh: line 4: `		case "$id" in

2 ~ $

Already gave instructions how to avoid these in: http://www.unix.com/302922954-post2.html
The code looks very identical to your previous code.

Please show some more effort (than just copy paste previous thread into a single file), you seem quite capable looking at your perl lines.

Thank you

---------- Post updated at 22:54 ---------- Previous update was at 22:33 ----------

However, to give you a hint on how to avoid the 'goto's, here is a little example:

#!/bin/bash
# Loop menu example
# 2014.10.31 by sea
################### 
#
#	Variables
#
	show_menu=true
	menu=( "Entry One" "Another two" "All good things are three" )
	func_show() { # "MESSAGE STRING"
	# Prints passed argument
	# Returns nothing
		printf '\n\t%s\n\n' "$1"
	}
#
#	Display & Action
#
	clear
	while $show_menu
	do	printf '#----------------------#\n%s\n' "Please select your task:"
		select entry in "${menu[@]}" Back
		do	case "$entry" in
			Back)		show_menu=false
					;;
			"Entry One")	func_show "first code (index id 0) :: $entry"
					;;
			"${menu[2]}")	func_show "third code :: ${menu[${#menu[@]}-1]}"
					;;
			*)		func_show "anything else (index id 1) :: $entry"
					;;
			esac
			break
		done
	done

Hope this helps

3

The code is similar in that it is the same basic structure with additional functionality trying to be added. Being new to awk and learning I tried following your example (thank you for that):

 #!/bin/bash			
show_menu=true
	menu=( "[yY]" "[nN]" )
	func_show() { # "MESSAGE STRING"
	# Prints passed argument
	# Returns nothing
		printf '\n\t%s\n\n' "$1"
	}
#
#	Display & Action
#
	clear
	while $show_menu
	do	printf '#----------------------#\n%s\n' "Are there additonal patients to be matched"
		select entry in "${menu[@]}" Back
		do	case "$entry" in
			Back)		show_menu=false
					;;
			"[yY]")	func_show "perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})' ${id}_${panel}_${OMR}.txt < ${id}_${panel}_${OMR}_Filtered.vcf > ${id}_matched.vcf (index id 0) :: $entry"
					;;
			"${menu[2]}")	func_show "printf "Does the file need to be converted  : " ; read id :: ${menu[${#menu[@]}-1]}"
					;;
			*)		
			esac
			break
		done
	done

This is just the first section of the script. If a "Y" response is given it will run a perl command, but if "N' is given it prompts the user and thats all. Is that correct? Thank you :).