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Combine shell files

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# 1  
Old 11-07-2014
Combine shell files
I am hoping the attached shell file is at least somewhat close to this.

Combining two shell file into one, where depending on the user input of"y" or "n" different commands are run. Thank you Smilie.

So first he user is asked for an ID to match, once the id is entered a script is run that uses that id. Following completion of the match the user is asked if there are additional files and depending on the response of "y' or "n" a script is run or another user prompt results.
newbatch.sh (1.7 KB) 
# 2  
Old 11-07-2014
"[yY]") func_show --> [yY]) func_show
Note the missing quotes.

They are missing since we want to do REGEX, not STRING compare.

Otherwise it will only execute if user entered a literal: [yY]
The 2nd case statement ${menu[2]} was back in the original threads, just as an example how to use the numeric value of the array.
However, it w/could work, IF the array item was properly formated -- it lacks the same cause as: yY, but in this case, just let away the quotes.

Also, but just from the looks of it, untested, your perl command needs some care regarding escape chars for the quotes within the perl command.

HINT: Try simpler scripts, get used to the syntax before doing such things you do since a week Smilie

Hope this gets you started.
Last edited by sea; 11-07-2014 at 03:11 PM..
# 3  
Old 11-08-2014
Made a few changes, hopefully they are right, but I am getting this error:
Code:
 $ bash ~/newbatch.sh
What is the id of the patient to be matched  : H62947
What panel: Epilepsy70
/home/cmccabe/newbatch.sh: line 5: syntax error near unexpected token `'C:\Users\cmccabe\Desktop\annovar''
/home/cmccabe/newbatch.sh: line 5: `            cd 'C:\Users\cmccabe\Desktop\annovar''


Code:
 
#!/bin/bash
	    printf "What is the id of the patient to be matched  : "; read id
	    printf "What panel: "; read panel
		case "$id" in
		cd 'C:\Users\cmccabe\Desktop\annovar'
	    	    OMR=Output_Mutation_Report
			perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$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
		;;
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
					;;
			[nN])	func_show "printf "Does the file need to be converted  : " ; read id :: ${menu[${#menu[@]}-1]}"
			while true
do
        printf "Enter ID  : " ; read id
		cd 'C:\Users\cmccabe\Desktop\annovar'
        [ -z "$id" ] && break
        [ "$id" = "end" ] && break
        perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput
done
					;;
			*)		
			esac
			break
		done
	done

Thanks Smilie.
# 4  
Old 11-08-2014
show_func expects a single string, therefor you must pass 'anything' you pass, as a single string.

What is the (terminal) output of (by itself):
Code:
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

And for the case itself, you need to embrace that commabd by : "$( CMD )" (including the quotes!), where CMD is the complete perl command, when called by itself returns exactly what you want.

Its not Windows Smilie
It linux, so try either one of:
  • $HOME/Desktop/annovar
  • /home/annovar/Desktop/annovar
  • /home/$USER/Desktop/annovar
  • $XDG_DESKTOP_DIR/annovar

Hope this helps
# 5  
Old 11-08-2014
The terminal output of the perl command is attached: it basically matches two separate files and combines them into one and excludes non-unique values. I am not sure I follow what you are saying about the syntax of the perl function, but made some changes.
I am using cygwin on a windows 7 machine Thank you very much Smilie

The cd line as is works if the shells are run separate but not when they are combined.

Code:
#!/bin/bash
	    printf "What is the id of the patient to be matched  : "; read id
	    printf "What panel: "; read panel
		case "$id" in
		cd 'C:\Users\cmccabe\Desktop\annovar'
	    	    OMR=Output_Mutation_Report
			perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$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
		;;
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 "$entry" in
			Back)		show_menu=false
					;;
			[yY])	perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$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
					;;
			[nN])	func_show "printf "Does the file need to be converted  : " ; read id :: ${menu[${#menu[@]}-1]}"
			while true
do
        printf "Enter ID  : " ; read id
		cd 'C:\Users\cmccabe\Desktop\annovar'
        [ -z "$id" ] && break
        [ "$id" = "end" ] && break
        perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput
done
					;;
			*)		
			esac
			break
		done
	done

example_matched.txt (24.9 KB) 
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