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# 8  
Old 03-12-2015
Wouldn't sth. like this make more sense (just an idea):
Code:
user choice 
|
v 
menu +> gjb2 -> name -> check -> position -> parse -> add2text -> additional? -> annovar -------+
  ^  |    ^                                                            v                        |
  |  |    +<---------------------------------------------------------<-+                        |
  |  |                                                                                          |
  |  +> mecp2 -> name -> check -> position -> parse -> add2text -> additional? -> annovar ------+
  |  |    ^                                                            v                        |
  |  |    +<---------------------------------------------------------<-+                        |
  |  |                                                                                          |
  |  +> phox2b -> name -> check -> position -> parse -> add2text -> additional? -> annovar -----+
  |  |    ^                                                            v                        |
  |  |    +<---------------------------------------------------------<-+                        |
  |  |                                                                                          |
  |  +> exit                                                                                    |
  +---------------------------------------------------------------------------------------------+

And it looks like there's quite some more potential to optimize.
# 9  
Old 03-12-2015
The 'gjb2' function as no closing bracket }.
And similar to RudiC, i'd highly recomend that the default behaviour of funtions should be return.

However, the menu function should be the only function calling others, which already is.
Also use either break or return to exit a case statement within a function.

As you already have split up the functionality to functions.
It is recomended to 'list' the functions, rather than calling 1 function which calls the other which calls another, which calls another - as one might produce unexpected behaviour.

For better readability, try to always use the same indention-blocks.
Usualy thats either 4 or 8 spaces or tabs.

hth

---------- Post updated at 22:53 ---------- Previous update was at 22:40 ----------
Since the follow up handling for all the 3 functions is identical, i'd attempt something like:
Code:
user choice 
|
|         +<--------------------------------------------------------------\
v         V                                                                \
menu +> gjb2  ->  \                                                         \
  ^  |             \                                                         \
  |  |              \                                                         \
  |  |               \                                                         ^
  |  +> mecp2 -------- +-> name -> check -> position -> parse -> add2text -> additional? -> annovar ------+
  |  |    ^           /                                                        v                          |
  |  |    +<-----------------------------------------------------------------<-+                          |
  |  |              /                                                         /                           |
  |  +> phox2b ->  /                                                         /                            |
  |  |    ^                                                                 /                             |
  |  |    +----------------------------------------------------------------/                              |
  |  |                                                                                                    |
  |  +> exit                                                                                              |
  +-------------------------------------------------------------------------------------------------------+

As on grab the data from one of the selected functions, and pass it to the follow up functions, which seem to be identical for each of the selectables...

hth
# 10  
Old 03-12-2015
The 3 user choices are virtually the same except for the sed which applies the correct transcript with the user choice. For example, if the choice is GJB2 then the NM_ is different then if the user choice was MECP2. I am out of my element here and am needing some expert assistance in making this code work. I am trying to learn all the terms, but admittedly slower it seems. Thank you Smilie.
# 11  
Old 03-13-2015
Make those 2 tasks, each a single function that works independant of each other.
Actualy you've already done so Smilie

Its all about the maintask function...
Code:
#!/usr/bin/env bash
#
#
# Functions
#
	function XY...
	...
	...
	
	function menu() {
	# Shows the menu and loops until Exit has been selected
	while true
		do
			printf "\n Welcome to annovar, 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  Exit\n\n
			==================================\n\n"

			printf "\t Your choice: "; read menu_choice

			case "$menu_choice" in
			1) maintask gjb2 ;;
			2) maintask mecp2 ;;
			3) maintask phox2b ;;
			4) printf "\n Bye! \n\n"; return 0 ;;
			*) printf "\n Invalid choice."; sleep 2 ;;
			esac
		done
	}
	function maintask() {
	# First and only argument expected to be the functions name!
		loop=true
		while $loop
		do
			$1       ### This would be one of:: gjb2 mecp2 phox2b
			check || break
			position
			convert
			add2text
			read -n1 -p "Do an additional patient for $1?"  yesno
			[ "$yesno" = y ] || loop=false
		done
		annovar
	}
#
# Action & Display
#
	menu

Hope this helps
# 12  
Old 03-13-2015
Thank you for the tips and help (very useful)... for the check function a file is created in C:/Users/cmccabe/Desktop/annovar/${id}.txt (attached), that has a warning column in it at $2 . If the variant has an error message in it can that be displayed as part of the check function? And if that field is blank "no errors" is displayed?

Also, in the echo -n what is the correct syntax to clear two or three files? Thank you Smilie



Code:
 check() {
    printf "\n\n"
    " warning from ${id}.txt in annovar directory"
    printf "Is the variant correct?  Y/N "; read match_choice

    case "$match_choice" in
        [yY]) id=""; position ;;
        [nN]) id=""; echo -n "" > C:/Users/cmccabe/Desktop/Python27/${id}.txt ; gjb2 ;;  
    esac
}

GJB-1_name.txt (558 Bytes) 
# 13  
Old 03-13-2015
Code:
    printf "\n\n"
    " warning from ${id}.txt in annovar directory"

Try:
Code:
    printf "\n\nwarning from ${id}.txt in annovar directory"

Just seeing i'm running out of time in RL...
I'm not good at awk yet, but maybe this could help to display the error message if one exists.
Code:
awk '
	NR==1
	if($2 != ""){
		print $2
	}'C:/Users/cmccabe/Desktop/Python27/${id}.txt

hth
This User Gave Thanks to sea For This Post:
cmccabe
# 14  
Old 03-13-2015
Quote:
Originally Posted by cmccabe
... ... ...

Also, in the echo -n what is the correct syntax to clear two or three files? Thank you Smilie

... ... ....
The command to create a regular file if it did not already exist or to truncate it to size zero if does already exist is:
Code:
> pathname

For more than one file, the syntax is:
Code:
> pathname1
> pathname2
...
> pathnameN

If the pathnames contain directories as well as a filename, that/those directory/directories must already exist for this to work. If you don't know if there might be missing directories, you can use:
Code:
mkdir -p "$(dirname pathname)" && > pathname

This User Gave Thanks to Don Cragun For This Post:
cmccabe
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