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Full Discussion: Filtering based on column values
Top Forums UNIX for Beginners Questions & Answers Filtering based on column values Post 302998224 by daashti on Saturday 27th of May 2017 10:56:36 AM
Old 05-27-2017
I will clean the mess and put the example in a better format.

Data
Code:
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT
chr1	65872	.	T	G	2480.51	.	AC=65;AN=92;SF=0,1;VRT=1	GT:GQ:DP:AD:PL
chr1	65893	.	G	A	433.77	.	AC=3;AN=4;SF=0,1;VRT=1	GT:GQ:PL:AD:DP
chr1	65898	.	T	C	2055.11	.	AC=7;AN=10;SF=0,1;VRT=1	GT:DP:AD:PL:GQ
chr1	69511	rs75062661	A	G	822333	.	AC=894;AN=934;SF=0,1;VRT=1	GT:GQ:DP:AD:PL
chr19	9088447	9088447	T	C	2420.41	.	AC=5;AN=10;SF=441,477,517,643,662;VRT=1	GT:GQ:DP:AD:PL
chr19	9072886	9072886	G	C	245.11	.	AC=5;AN=10;SF=448,498,500,741,778;VRT=1	GT:GQ:PL:AD:DP
chr7	149484550	149484550	G	A	305.11	.	AC=5;AN=10;SF=606,704,723,736,763;VRT=1	GT:DP:AD:PL:GQ
chr7	149482784	149482784	C	T	822	.	AC=5;AN=10;SF=472,478,684,708,799;VRT=1	GT:GQ:DP:AD:PL

After filtering
Code:
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT
chr19	9088447	9088447	T	C	2420.41	.	AC=5;AN=10;SF=441,477,517,643,662;VRT=1	GT:GQ:DP:AD:PL
chr19	9072886	9072886	G	C	245.11	.	AC=5;AN=10;SF=448,498,500,741,778;VRT=1	GT:GQ:PL:AD:DP
chr7	149484550	149484550	G	A	305.11	.	AC=5;AN=10;SF=606,704,723,736,763;VRT=1	GT:DP:AD:PL:GQ
chr7	149482784	149482784	C	T	822	.	AC=5;AN=10;SF=472,478,684,708,799;VRT=1	GT:GQ:DP:AD:PL

 

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LEARN ABOUT DEBIAN

rgb2pct

rgb2pct(1)						      General Commands Manual							rgb2pct(1)

NAME

       rgb2pct - rgb2pct.py Convert a 24bit RGB image to 8bit paletted

SYNOPSIS

       rgb2pct.py [-n colors | -pct palette_file] [-of format] source_file dest_file

DESCRIPTION

       This utility will compute an optimal pseudo-color table for a given RGB image using a median cut algorithm on a downsampled RGB histogram.
       Then it converts the image into a pseudo-colored image using the color table. This conversion utilizes Floyd-Steinberg dithering (error
       diffusion) to maximize output image visual quality.

       -n colors:
	   Select the number of colors in the generated color table. Defaults to 256. Must be between 2 and 256.

       -pct palette_file:
	   Extract the color table from palette_file instead of computing it. Can be used to have a consistant color table for multiple files. The
	   palette_file must be a raster file in a GDAL supported format with a palette.

       -of format:
	   Format to generated (defaults to GeoTIFF). Same semantics as the -of flag for gdal_translate. Only output formats supporting
	   pseudocolor tables should be used.

       source_file:
	   The input RGB file.

       dest_file:
	   The output pseudo-colored file that will be created.

       NOTE: rgb2pct.py is a Python script, and will only work if GDAL was built with Python support.

EXAMPLE

       If it is desired to hand create the palette, likely the simpliest text format is the GDAL VRT format. In the following example a VRT was
       created in a text editor with a small 4 color palette with the RGBA colors 238/238/238/255, 237/237/237/255, 236/236/236/255 and
       229/229/229/255.

       % rgb2pct.py -pct palette.vrt rgb.tif pseudo-colored.tif
       % more < palette.vrt
       <VRTDataset rasterXSize="226" rasterYSize="271">
	 <VRTRasterBand dataType="Byte" band="1">
	   <ColorInterp>Palette</ColorInterp>
	   <ColorTable>
	     <Entry c1="238" c2="238" c3="238" c4="255"/>
	     <Entry c1="237" c2="237" c3="237" c4="255"/>
	     <Entry c1="236" c2="236" c3="236" c4="255"/>
	     <Entry c1="229" c2="229" c3="229" c4="255"/>
	   </ColorTable>
	 </VRTRasterBand>
       </VRTDataset>

AUTHOR

       Frank Warmerdam warmerdam@pobox.com

GDAL
								  Tue Sep 18 2012							rgb2pct(1)
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