Rewrite sed to perl or run sed in perl Post: 302940888

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Top Forums Shell Programming and Scripting Rewrite sed to perl or run sed in perl Post 302940888 by cmccabe on Thursday 9th of April 2015 04:10:45 PM

04-09-2015

Registered User

Two variants are inputted by the user and written to one file (out_position.txt). Then the below parser is used on that file. Depending on the input line one of the parse conditions is used. So, for the "del" in line 1 of the input file the # deletion is used. For the "delins" on line 2 the # indel is used. So the resulting output of the parsed file would be two lines (it is 3 now). I am not sure how to fix it but it looks like the while may be the issue, bit removing it doesnt result in the desired output. Thank you Smilie

Code:

 perl -ne 'next if $. == 1;
	if(/.*del([A-Z]+)ins([A-Z]+).*NC_0{4}([0-9]+).*g\.([0-9]+)_([0-9]+)/)   # indel
{
        print join("\t", $3, $4, $5, $1, $2), "\n";
}
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+)/g) {                                            # conditional parse
                ($num1, $num2, $common) = ($1, $2, $3);
                $num3 = $num2;
                if    ($common =~ /^([A-Z])>([A-Z])$/)   { ($ch1, $ch2) = ($1, $2) }              # SNP
                elsif ($common =~ /^del([A-Z])$/)        { ($ch1, $ch2) = ($1, "-") }             # deletion
                elsif ($common =~ /^ins([A-Z])$/)        { ($ch1, $ch2) = ("-", $1) }             # insertion
                elsif ($common =~ /^_(\d+)del([A-Z]+)$/) { ($num3, $ch1, $ch2) = ($1, $2, "-") }  # multi deletion
				elsif ($common =~ /^_(\d+)ins([A-Z]+)$/) { ($num3, $ch1, $ch2) = ("-", $1, $2) }  # multi insertion
                printf ("%d\t%d\t%d\t%s\t%s\n", $num1, $num2, $num3, $ch1, $ch2);                 # output
                map {undef} ($num1, $num2, $num3, $common, $ch1, $ch2);
            }
           ' C:/Users/cmccabe/Desktop/annovar/out_position.txt > C:/Users/cmccabe/Desktop/annovar/out_parse.txt

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shtool-subst

SHTOOL-SUBST.TMP(1)					      GNU Portable Shell Tool					       SHTOOL-SUBST.TMP(1)

NAME

       shtool-subst - GNU shtool sed(1) substitution operations

SYNOPSIS

       shtool subst [-v|--verbose] [-t|--trace] [-n|--nop] [-w|--warning] [-q|--quiet] [-s|--stealth] [-i|--interactive] [-b|--backup ext]
       [-e|--exec cmd] [-f|--file cmd-file] [file] [file ...]

DESCRIPTION

       This command applies one or more sed(1) substitution operations to stdin or any number of files.

OPTIONS

       The following command line options are available.

       -v, --verbose
	   Display some processing information.

       -t, --trace
	   Enable the output of the essential shell commands which are executed.

       -n, --nop
	   No operation mode. Actual execution of the essential shell commands which would be executed is suppressed.

       -w, --warning
	   Show warning on substitution operation resulting in no content change on every file. The default is to show a warning on substitution
	   operations resulted in no content change on all files.

       -q, --quiet
	   Suppress warning on substitution operation resulting in no content change.

       -s, --stealth
	   Stealth operation. Preserve timestamp on file.

       -i, --interactive
	   Enter interactive mode where the user has to approve each operation.

       -b, --backup ext
	   Preserve backup of original file using file name extension ext.  Default is to overwrite the original file.

       -e, --exec cmd
	   Specify sed(1) command directly.

       -f, --file cmd-file
	   Read sed(1) command from file.

EXAMPLE

	#   shell script
	shtool subst -i -e 's;(c) ([0-9]*)-2000;(c) 1-2001;' *.[ch]

	#    RPM spec-file
	%install
	    shtool subst -v -n 
		-e 's;^(prefix=).*;1 $RPM_BUILD_ROOT%{_prefix};g' 
		-e 's;^(sysconfdir=).*;1 $RPM_BUILD_ROOT%{_prefix}/etc;g' 
		`find . -name Makefile -print`
	    make install

HISTORY

       The GNU shtool subst command was originally written by Ralf S.  Engelschall <rse@engelschall.com> in 2001 for GNU shtool.  It was prompted
       by the need to have a uniform and convenient patching frontend to sed(1) operations in the OpenPKG package specifications.

SEE ALSO

       shtool(1), sed(1).

18-Jul-2008							   shtool 2.0.8 					       SHTOOL-SUBST.TMP(1)