Adding a prefix to a column using awk/sed commands Post: 302484877

Sponsored Content

Operating Systems Linux Adding a prefix to a column using awk/sed commands Post 302484877 by bjorngill on Monday 3rd of January 2011 01:42:29 PM

01-03-2011

Registered User

I have a question regarding extracting information from csv file. I have very large file with 7 columns and few thousand rows. I would like to search using one or two of these columns and extract information into a text file.

For example, I want to search for Column "Name" for mir-19b and extract all the columns.

Here is the sample csv file.

Code:

Small RNA	                      Expression values	Length	Count	Name	                       Match type	      Mismatches
TGTGCAAATCCATGCAAAACTGA	43,919	23	43,919	mir-19b	Mature	   0
CAGTGCAATATTAAAAGGGCAT 	42,583	22	42,583	mir-130c-1//mir-130c-2	Mature	0
GTGAAATGTTCAGGACCACTTG	        28,357	22	28,357	mir-203b	Mature	0
TTCCCTTTGTCATCCTATGCCT	        27,297	22	27,297	mir-204-1//mir-204-2	Mature	0
TAAAGTGCTTATAGTGCAGGTAG	25,594	23	25,594	mir-20a	Mature	1
CAGTGCAATAATGAAAGGGCAT	23,802	22	23,802	mir-130b	Mature	0
TCCTTCATTCCACCGGAGTCTG	       17,791	22	17,791	mir-205	Mature	2
TGTGCAAATCTATGCAAAACTGA	17,501	23	17,501	mir-19a	Mature	0
TACCCTGTAGATCCGGATTTGT	       17,431	22	17,431	mir-10c	Mature	0
CAGTGCAATAGTATTGTCATAGCAT	17,203	25	17,203	mir-301c	Precursor	0
TGGAATGTAAGGAAGTGTGTGG	16,786	22	16,786	mir-206-1//mir-206-2	Mature	0
GTGAAATGTTTAGGACCACTTG	       16,657	22	16,657	mir-203a	Mature	0
TGTGCAAATCCATGCAAAACTCG	14,449	23	14,449	mir-19c	Mature	0

Any suggestions in using perl or linux commands will be helpful.

Last edited by joeyg; 01-03-2011 at 04:07 PM.. Reason: break out the file

bjorngill

View Public Profile for bjorngill

Find all posts by bjorngill

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk-adding a column to a file

Hello Friends, i used awk to sum up total size of files under a directory (with the help of examples, threads here). ls -l | awk '/^-/ {total += $5} END {printf "%15.0f\n",total}' >> total.txt After each execution of the script total result is appended into a text file: 7010 7794 8890 ...

2. Shell Programming and Scripting

sed/awk-adding numeric to a column

I have a txt file as follows Code: Oct 1 file1 4144 Oct 1 file23 5170 Oct 2 file5 3434 Oct 21 file56 2343 I need to add a new column by marking the right log file from current directory. For example populate like this. Please not in the second columt for "1" it has...

3. UNIX for Dummies Questions & Answers

Adding a column with the row number using awk

Is there anyway to use awk to add a first column to my data that automatically goes from 1 to n , where n is the numbers of my rows?:confused:

4. Shell Programming and Scripting

Adding column using awk

Hello everyone, I have a file with the following structure: abc xyz 111 222 agf hjhf 787 799 tht yah 878 898 ... ... ... ... ... ... ... ... ... ... ... ... I want to add a column (with a fixed value of 1000) at the end such that it becomes: abc xyz 111 222 1000 agf hjhf 787...

5. Shell Programming and Scripting

Adding prefix to the values in the script

Hi, test.txt contains below values 1 2 3 4 5 Desired output: 'TT.1', 'TT.2', 'TT.3', 'TT.4', 'TT.5' Last value should not contain the comma after the value. Below is the script which i have tried. I'm using Linux. #!/bin/bash for i in $test.txt

6. UNIX for Dummies Questions & Answers

Adding Filename as column using sed

Hi , Can any one please tell me, how can we add the file name as column using sed. right now we are using the below awk command for adding the file name as column but when we are calling this script from datastage it is deleting the file data..very weird raised a support ticket with datastage....

7. Shell Programming and Scripting

AWK adding prefix/suffix to list of strings

75 103 131 133 138 183 197 221 232 234 248 256 286 342 368 389 463 499 524 538

8. Shell Programming and Scripting

Adding a specified value to a specified column - awk?

Hi everyone! I sometimes need to do some simple arithmetics, like adding a number to a certain column of a file. So I wrote a small function in the .bashrc file, which looks like this shifter() { COL=$1 VAL=$2 FILE=$3 cp $FILE $FILE.shifted awk 'NF==4 {$(( $COL )) = $(( $COL ))...

9. UNIX for Dummies Questions & Answers

awk adding counts together from column

Hello Im new treat me nicely, I have a headache :) I have a script that seemed to work now it doesnt anyway, the last part is adding counts of unique items in a csv file eg 05492U34 38 05492U34 47 two columns, (many different values like this in file) i want...

10. Shell Programming and Scripting

Need to add prefix using sed or awk from cat the file

I need the use sed or AWK using cat the file Node1 TDEV RW 1035788 TDEV RW 1035788 Server1 TDEV RW 69053 Server2 TDEV RW 69053 TDEV RW 103579 Server3 TDEV RW 69053 server4 RDF1+TDEV RW 69053 RDF1+TDEV RW 517894 RDF1+TDEV RW 621473 server6 TDEV RW 34526 TDEV RW 34526

LEARN ABOUT SUSE

png2yuv

png2yuv(1)							MJPEG tools manual							png2yuv(1)

NAME

       png2yuv - Convert PNG images to the YUV4MPEG stream format.

SYNOPSIS

       png2yuv [-b num] [-f num] [-I num] [-L num] [-n num] [-l num] [-j filename]

DESCRIPTION

       png2yuv decompresses a sequence of PNG files and pipes the image data to stdout as a YUV4MPEG2 stream.  Any 8bit/pixel PNG format supported
       by libpng can be read.  stdout will be filled with the YUV4MPEG movie data stream, so be prepared to pipe it on to mpeg2enc or to write	it
       into a file.

       This tool is incomplete.  The alternative utility you are probably looking for is ppmtoy4m(1), which is also included in MJPEGtools.

OPTIONS

       png2yuv accepts the following options:

       -b num
	    Frame offset:  skip output of the first 'num' frames.  (default: 0)

       -f num
	    Set the frame rate of stream accepts the same numbers. Not default, this option has to be specified.

       -I num
	    interlacing mode: p = none / progressive
	    t = top field first
	    b = bottom field first
	    No default, this option has to be specified.

       -L num
	    0 = non-interleaved (two successive fields per PNG file)
	    1 = interleaved fields

       -l num
	    Specifies the number of loops (default: 0 loops )

       -S samp_mode
	    chroma subsampling mode, only for professionals, for more info see ppmtoy4m and the YUV guide on http://www.mir.com/DMG/.
	    default: 420_jpeg
	    When  this	option	is not used the given range of images is only processed once. If you use this option and as number 1, jpeg2yv will
	    loop forever writing the image to stdout. When you use n > 1 it will loop. n-time till it finishes.

       -n num
	    Specifies the nummber of frames to process. (default: all = -1)

       -j {1}%{2}d{3}
	    Read PNG frames with the name components as follows:
	     {1} PNG filename prefix (e g: picture_ )
	     {2} Counting placeholder (like in C, printf, eg 06 ))
	     {3} File extension. Something like this: .png A correct description of the files could look like this: picture_%06d.png

       -v num
	    Verbosity level (0, 1 or 2)

BUGS

       The frame rate description does not seem to be up to date. The NTSC integer ratios are not supported (use floating point instead). As work-
       around  specify	a  PAL	(25)  or native FILM (24) and set the right frame rate in mpeg2enc with the -F option.	Interlaced handling is not
       implemented yet.

AUTHOR

       This man page was written by Gernot Ziegler.
       If you have questions, remarks, problems or you just want to contact the developers, the main mailing list for the MJPEG-tools is:
	 mjpeg-users@lists.sourceforge.net

       For more info, see our website at
	      http://mjpeg.sourceforge.net

SEE ALSO

       mjpegtools(1), mpeg2enc(1), ppmtoy4m(1), yuv2lav(1), yuvdenoise(1), yuvmedianfilter(1), yuvscaler(1)

MJPEG Linux Square						  2 February 2003							png2yuv(1)

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk-adding a column to a file

Discussion started by: EAGL�

2. Shell Programming and Scripting

sed/awk-adding numeric to a column

Discussion started by: gubbu

3. UNIX for Dummies Questions & Answers

Adding a column with the row number using awk

Discussion started by: cosmologist

4. Shell Programming and Scripting

Adding column using awk

Discussion started by: ad23