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

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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

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LEARN ABOUT MOJAVE

column

COLUMN(1)						    BSD General Commands Manual 						 COLUMN(1)

NAME

     column -- columnate lists

SYNOPSIS

     column [-tx] [-c columns] [-s sep] [file ...]

DESCRIPTION

     The column utility formats its input into multiple columns.  Rows are filled before columns.  Input is taken from file operands, or, by
     default, from the standard input.	Empty lines are ignored.

     The options are as follows:

     -c      Output is formatted for a display columns wide.

     -s      Specify a set of characters to be used to delimit columns for the -t option.

     -t      Determine the number of columns the input contains and create a table.  Columns are delimited with whitespace, by default, or with
	     the characters supplied using the -s option.  Useful for pretty-printing displays.

     -x      Fill columns before filling rows.

ENVIRONMENT

     The COLUMNS, LANG, LC_ALL and LC_CTYPE environment variables affect the execution of column as described in environ(7).

EXIT STATUS

     The column utility exits 0 on success, and >0 if an error occurs.

EXAMPLES

	   (printf "PERM LINKS OWNER GROUP SIZE MONTH DAY " ; 
	   printf "HH:MM/YEAR NAME
" ; 
	   ls -l | sed 1d) | column -t

SEE ALSO

     colrm(1), ls(1), paste(1), sort(1)

HISTORY

     The column command appeared in 4.3BSD-Reno.

BUGS

     Input lines are limited to LINE_MAX (2048) bytes in length.

BSD
								   July 29, 2004							       BSD

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