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UNIX for Advanced & Expert Users
Map snps into a ref gene file
Post 302989929 by marwah on Thursday 19th of January 2017 09:52:50 PM
01-19-2017
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I had two files 1.txt 2.txt. I want a 3rd file(o/p) 3.txt like below (using awk)
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11 a1
12 a2
13 a3
14 a4
15 a5
16 a6
17 a7
18 a8
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FILE1
abc:xxx:abc:123:wer:AAA:12
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AAA:12:SET1:R1
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Hi, my problem is that I have two files. File no. 1 is a gff text file (say gi1) that has gene information like :
********************
gene 39389788..39395643
/gene="RPSA"
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I had two files 1.txt 2.txt. I want a 3rd file(o/p) 3.txt like below based on the common elements from the first coulmns of 1.txt and 2.txt.
1.txt
11
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21
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Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
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I am trying to modify the awk below to include the gene name ($5) for each target and can not seem to do so. Also, I'm not sure the calculation is right (average of all targets that are the same is $4 using the values in $7)? Thank you :).
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I have the following Snps data
CHROM POS ID
chr7 78599583 rs987435
chr15 33395779 rs987436
chr1 189807684 rs987437
chr20 33907909 rs987438
chr12 75664046 rs987439
and the following gene data
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LEARN ABOUT V7
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)