Rewrite sed to perl or run sed in perl Post: 302940751

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Top Forums Shell Programming and Scripting Rewrite sed to perl or run sed in perl Post 302940751 by cmccabe on Wednesday 8th of April 2015 05:08:22 PM

04-08-2015

Registered User

Rewrite sed to perl or run sed in perl

I am having trouble re-writing this sed code

Code:

 sed -nr 's/.*del([A-Z]+)ins([A-Z]+).*NC_0{4}([0-9]+).*g\.([0-9]+)_([0-9]+).*/\3\t\4\t\5\t\1\t\2/p' C:/Users/cmccabe/Desktop/Python27/out_position.txt > C:/Users/cmccabe/Desktop/Python27/out_parse.txt

in perl Basically, what the code does is parse text from two fields of a file.

The other option is integrating the sed into the existing perl , but I am not sure how. Thank you Smilie

Code:

 perl -ne 'next if $. == 1;
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+)/g) {                                            # conditional parse
                ($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/Python27/out_position.txt > C:/Users/cmccabe/Desktop/Python27/out_parse.txt

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diffmk

diffmk(1)							   User Commands							 diffmk(1)

NAME

       diffmk - mark differences between versions of a troff input file

SYNOPSIS

       diffmk oldfile newfile markedfile

DESCRIPTION

       diffmk  compares  two versions of a file and creates a third version that includes "change mark" (.mc) commands for nroff(1) and  troff(1).
       oldfile and newfile are the old and new versions of the file. diffmk generates markedfile, which,  contains  the  text  from  newfile  with
       troff(1) "change mark" requests (.mc) inserted where  newfile differs from  oldfile. When markedfile is formatted, changed or inserted text
       is shown by  | at the right margin of each line. The position of deleted text is shown by a single *.

USAGE

       See largefile(5) for the description of the behavior of diffmk when encountering files greater than or equal to 2 Gbyte ( 2^31 bytes).

EXAMPLES

       Example 1 An example of the diffmk command.

       diffmk can also be used in conjunction with the proper  troff requests to produce program listings with marked changes.	In  the  following
       command line:

	 example% diffmk old.c new.c marked.c ; nroff reqs marked.c | pr

       the file reqs contains the following troff requests:

	 .pl 1
	 .ll 77
	 .nf
	 .eo
	 .nh

       which eliminate page breaks, adjust the line length, set no-fill mode, ignore escape characters, and turn off hyphenation, respectively.

       If the characters  | and * are inappropriate, you might run  markedfile through	sed(1) to globally change them.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWdoc			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       diff(1), nroff(1), sed(1), troff(1), attributes(5), largefile(5)

BUGS

       Aesthetic  considerations  may  dictate	manual	adjustment of some output. File differences involving only formatting requests may produce
       undesirable output, that is, replacing .sp by .sp 2 will produce a "change mark" on the preceding or following line of output.

SunOS 5.11							    14 Sep 1992 							 diffmk(1)