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Full Discussion: Perl to parse
Top Forums Shell Programming and Scripting Perl to parse Post 302939350 by durden_tyler on Tuesday 24th of March 2015 11:04:39 PM
Old 03-25-2015
Code:
$
$ cat out_position.txt
Input Variant   Errors  Chromosomal Variant     Coding Variant(s)
NM_004004.5:c.283G>C            NC_000013.10:g.20763438C>G      NM_004004.5:c.283G>C    XM_005266354.1:c.283G>C XM_005266355.1:c.283G>C XM_005266356.1:c.283G>C
NM_004004.5:c.79G>C             NC_000013.10:g.20763642C>G      NM_004004.5:c.79G>C     XM_005266354.1:c.79G>C  XM_005266355.1:c.79G>C  XM_005266356.1:c.79G>C
NM_004004.5:c.35delG            NC_000013.10:g.20763686delC     NM_004004.5:c.35delG    XM_005266354.1:c.35delG XM_005266355.1:c.35delG XM_005266356.1:c.35delG
$
$
$ # Method 1 : Using a non-capturing grouping in Perl regular expression
$ perl -ne 'next if $. == 1;
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(?:del)*([A-Z])>*([A-Z]*)/g) {
                printf ("%d\t%d\t%d\t%s\t%s\n", $1, $2, $2, $3, $4 || "-");
            }
           ' out_position.txt
13      20763438        20763438        C       G
13      20763642        20763642        C       G
13      20763686        20763686        C       -
$
$
$ # Method 2 : Using more elaborate but plain-vanilla regular expressions
$ perl -ne 'next if $. == 1;
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+[A-Z])/g) {
                ($num1, $num2, $common) = ($1, $2, $3);
                if ($common =~ /([A-Z])>([A-Z])/) {
                    ($ch1, $ch2) = ($1, $2)
                } elsif ($common =~ /del([A-Z])/) {
                    ($ch1, $ch2) = ($1, "-")
                }
                printf ("%d\t%d\t%d\t%s\t%s\n", $num1, $num2, $num2, $ch1, $ch2);
                map {undef} ($num1, $num2, $common, $ch1, $ch2);
            }
           ' out_position.txt
13      20763438        20763438        C       G
13      20763642        20763642        C       G
13      20763686        20763686        C       -
$
$

This User Gave Thanks to durden_tyler For This Post:
cmccabe
 

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LEARN ABOUT OSX

ppmtosixel

ppmtosixel(1)						      General Commands Manual						     ppmtosixel(1)

NAME

       ppmtosixel - convert a portable pixmap into DEC sixel format

SYNOPSIS

       ppmtosixel [-raw] [-margin] [ppmfile]

DESCRIPTION

       Reads  a  portable  pixmap  as input.  Produces sixel commands (SIX) as output.	The output is formatted for color printing, e.g. for a DEC
       LJ250 color inkjet printer.

       If RGB values from the PPM file do not have maxval=100, the RGB values are rescaled.  A printer control header and a color assignment table
       begin the SIX file.  Image data is written in a compressed format by default.  A printer control footer ends the image file.

OPTIONS

       -raw   If  specified,  each  pixel  will  be explicitly described in the image file.  If -raw is not specified, output will default to com-
	      pressed format in which identical adjacent pixels are replaced by "repeat pixel" commands.  A raw file is often an order	of  magni-
	      tude larger than a compressed file and prints much slower.

       -margin
	      If  -margin  is not specified, the image will be start at the left margin (of the window, paper, or whatever).  If -margin is speci-
	      fied, a 1.5 inch left margin will offset the image.

PRINTING

       Generally, sixel files must reach the printer unfiltered.  Use the lpr -x option or cat filename > /dev/tty0?.

BUGS

       Upon rescaling, truncation of the least significant bits of RGB values may result in poor color conversion.  If the original PPM maxval was
       greater	than  100,  rescaling  also reduces the image depth.  While the actual RGB values from the ppm file are more or less retained, the
       color palette of the LJ250 may not match the colors on your screen.  This seems to be a printer limitation.

SEE ALSO

       ppm(5)

AUTHOR

       Copyright (C) 1991 by Rick Vinci.

								   26 April 1991						     ppmtosixel(1)
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