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Full Discussion: Parsing a list of data
Top Forums UNIX for Dummies Questions & Answers Parsing a list of data Post 302682713 by baika on Monday 6th of August 2012 05:55:25 PM
Old 08-06-2012
Parsing a list of data
Hi
I have a vcf file with 20000 lines, it looks like this-
Code:
23	122691	.	C	1345.09	PASS
33	122961	.	C	833.45	PASS
43	122970	.	A	689.75	PASS
53	123009	.	T	118.99	PASS
63	123033	.	T	46.85	PASS
73	123042	.	A	127.51	PASS
83	123060	.	T	299.64	PASS
93	123081	.	T	299.64	PASS
103	123105	.	C	210.83	PASS
113	123108	.	G	139.65	PASS
123	123147	.	A	132.79	PASS
133	123162	.	A	120.25	PASS
143	123171	.	G	174.31	SnpCluster
153	123177	.	C	109.46	SnpCluster
163	123180	.	G	146.46	SnpCluster
173	123282	.	A	10.22	LowQual;SnpCluster
183	123285	.	A	15.92	LowQual;SnpCluster
193	123288	.	G	15.92	LowQual;SnpCluster
203	123300	.	A	1327.57	PASS
213	123301	.	G	955.37	PASS
223	123321	.	A	708.37	PASS
233	123363	.	G	131.35	PASS
243	123366	.	A	742.72	PASS
253	123407	.	C	574.47	SnpCluster
263	123408	.	T	574.47	SnpCluster
273	123411	.	A	696.24	SnpCluster
283	123420	.	G	89.09	PASS
293	123426	.	A	690.57	PASS
303	123474	.	A	59.45	PASS
313	123477	.	C	576.22	PASS
323	123489	.	G	396.59	PASS
333	123651	.	C	79.36	PASS
343	123705	.	C	908.33	PASS
353	436405	.	C	969.24	PASS
363	436472	.	G	969.24	PASS
373	436614	.	C	1052.76	PASS
383	436684	.	A	718.68	PASS
393	436748	.	C	676.92	PASS
403	436760	.	T	718.68	PASS
413	436798	.	A	927.48	PASS

I want to filter this file based on the values/ranges in column 2. For example, in a new file I do not want lines with values 123171-123407, and 123651-436748 in column2. Please suggest any simple unix command.

Thanks
Last edited by Scott; 08-06-2012 at 06:59 PM.. Reason: Please use code tags, and a meaningful subject title to describe your problem. Thank you.
 

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LEARN ABOUT MINIX

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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