05-30-2011
Hi,
Thanks for the reply.. but some how the code does not work.
My sample files are (example I list only file 1) The file 2 and file 3 have columns 1&3 similar but the counts in the 2nd column differ.
chr22_16256301_16256350 0 PATF
chr22_16256351_16256400 0 CFTY
chr22_16256401_16256450 0 ATGC
chr22_16256451_16256500 0 RBRH
chr22_16256501_16256550 0 THGC
chr22_16256551_16256600 0 OTHV
When I tried the code above it listed all the rows in top.10 output file and did not produce any rest.90 file as output.
Thanks,
Diya
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pnmcut(1) General Commands Manual pnmcut(1)
NAME
pnmcut - cut a rectangle out of a portable anymap
SYNOPSIS
pnmcut [-left leftcol] [-right rightcol] [-top toprow] [-bottom bottomrow] [-width width] [-height height] [-pad] [-verbose] [ left top
width height ] [pnmfile]
All options may be abbreviated to the shortest unique prefix.
DESCRIPTION
Reads a PBM, PGM, or PPM image as input. Extracts the specified rectangle, and produces the same kind of image as output.
There are two ways to specify the rectangle to cut: arguments and options. Options are easier to remember and read, more expressive, and
allow you to use defaults. Arguments were the only way available before July 2000.
If you use both options and arguments, the two specifications get mixed in an unspecified way.
To use options, just code any mixture of the -left, -right, -top, -bottom, -width, and -height options. What you don't specify defaults.
It is an error to overspecify, i.e. to specify all three of -left, -right, and -width or -top, -bottom, and -height.
To use arguments, specify all four of the left, top, width, and height arguments. left and top have the same effect as specifying them as
the argument of a -left or -top option, respectively. width and height have the same effect as specifying them as the argument of a -width
or -height option, respectively, where they are positive. Where they are not positive, they have the same effect as specifying one less
than the value as the argument to a -right or -bottom option, respectively. (E.g. width = 0 makes the cut go all the way to the right
edge). Before July 2000, negative numbers were not allowed for width and height.
Input is from Standard Input if you don't specify the input file pnmfile.
Output is to Standard Output.
OPTIONS
-left The column number of the leftmost column to be in the output. If a nonnegative number, it refers to columns numbered from 0 at the
left, increasing to the right. If negative, it refers to columns numbered -1 at the right, decreasing to the left.
-right The column number of the rightmost column to be in the output, numbered the same as for -left.
-top The row number of the topmost row to be in the output. If a nonnegative number it refers to rows numbered from 0 at the top,
increasing downward. If negative, it refers to columns numbered -1 at the bottom, decreasing upward.
-bottom
The row number of the bottom-most row to be in the output, numbered the same as for -top.
-width The number of columns to be in the output. Must be positive.
-height
The number of rows to be in the output. Must be positive.
-pad If the rectangle you specify is not entirely within the input image, pnmcut fails unless you also specify -pad. In that case, it
pads the output with black up to the edges you specify. You can use this option if you need to have an image of certain dimensions
and have an image of arbitrary dimensions.
pnmpad can also fill an image out to a specified dimension, and gives you more explicit control over the padding.
-verbose
Print information about the processing to Standard Error.
SEE ALSO
pnmcrop(1), pnmpad(1), pnmcat(1), pgmslice(1), pnm(5)
AUTHOR
Copyright (C) 1989 by Jef Poskanzer.
29 June 2000 pnmcut(1)