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Top Forums UNIX for Dummies Questions & Answers Help with BASH/AWK queries .... Post 302477394 by Fahmida on Saturday 4th of December 2010 11:08:45 PM
Old 12-05-2010
Help with BASH/AWK queries ....

Hi Everyone,

I have an input file in the following format:
score.file1.txt
HTML Code:
contig00045 length=566   numreads=19    1047    0.0
contig00055 length=524   numreads=7    793    0.0
contig00052 length=535   numreads=10    607    e-176
contig00072 length=472   numreads=46    571    e-165
contig00019 length=667   numreads=5    474    e-136
I've a second file:
data.file1.txt
HTML Code:
>contig00045 length=566   numreads=19
GGGCTGACGTGCCGCTAATACGACTCACTATAGGGAGAGCATAAAACACG
CCTCCTGAGCTGCAGCAGAAAAAGAGACTCCCCTTGAGCTTTCAGATTGA
>contig00055 length=524   numreads=7
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGGAGGGAGGAT
GCTGGAC
>contig00052 length=535   numreads=10
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGGGATGTCCAC
AGGCAGAGGGATGTCCACAGGCAGAGGGATGCCACAGGCA
>contig00072 length=472   numreads=46
TTTAGCTGCTTTCCCCCGGAGGAGATTTGAATTCCGGTGAAATCCAGGCT
TTGTTCATTTTAATAAGCGTCAGCCTGTCAGCGCTGTCAGTTGACAGGCG
>contig00019 length=667   numreads=5
TATAGGGAGAGTGGCATTCTAATAACAGGGGACGGGGGCAGAGGACTCTC
GCTGACCGTCCCATGTAAGGGTGGTGTCGGAT
This file contains a header (>contig00045 length=566 numreads=19) followed by few lines of sequence.

In the first file (score.file1.txt), for each row the fourth column is score1(1047, 793, 607,571 etc.) and 5th column is score2 (0.0, 0.0, e-176, e-165 etc.).
I would like to extract those TWO data (from data.file1.txt) based on TOP score1 and if their score2 is NOT 0.0.

For example based on the above data, my desired output is:
output.file1.txt
HTML Code:
>contig00052 length=535   numreads=10
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGGGATGTCCAC
AGGCAGAGGGATGTCCACAGGCAGAGGGATGCCACAGGCA
>contig00072 length=472   numreads=46
TTTAGCTGCTTTCCCCCGGAGGAGATTTGAATTCCGGTGAAATCCAGGCT
TTGTTCATTTTAATAAGCGTCAGCCTGTCAGCGCTGTCAGTTGACAGGCG
Thanks in advance.
 

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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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