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Top Forums Shell Programming and Scripting selecting specific fields in a file (maybe with sed?) Post 302491295 by menenuh on Thursday 27th of January 2011 05:57:02 AM
Old 01-27-2011
selecting specific fields in a file (maybe with sed?)

Hi,

I have a file with following lines:
Code:
chr1    10   AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=23.00;MQ0=0;QD=14.33;SB=-10.01
chrX    18   AB=0.52;AC=1;AF=0.50;AN=2;DP=203;DS;Dels=0.00;HRun=0;HaplotypeScore=20.01;MQ=15.63;MQ0=85;QD=12.80;SB=-1289.58

I need to extract 4 fields from these lines, the 1st and 2nd column, and AF and DP values. I could have used cut command if AF and DP were printed in the same order, but this is not the case.

I think forming columns (by separating the 3rd line) and removing any column not containing AF or DP would be a nice solution, but I am not an expert on sed. I tried a couple of commands, but to no avail.

Last edited by Yogesh Sawant; 01-27-2011 at 07:45 AM.. Reason: added code tags
 

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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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