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Full Discussion: Change directory error
Top Forums Shell Programming and Scripting Change directory error Post 302924531 by cmccabe on Monday 10th of November 2014 10:37:07 AM
Old 11-10-2014
Change directory error

bash ~/match.sh runs fine.
Code:
#!/bin/bash
	printf "Enter ID  : "; read id
	printf "What panel: "; read panel
		cd 'C:\Users\cmccabe\Desktop\annovar'
			[ -z "$id" ] && break
			[ "$id" = "end" ] && break
		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

I am trying to combine shells: bash ~/newbatch.sh
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

I am sure the code needs work, but why does it throw an error in the underlined part when it was fine before? Thanks Smilie.

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''

 

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