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Adding a prefix to a column using awk/sed commands


 
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# 1  
Old 12-29-2010
Adding a prefix to a column using awk/sed commands

Hello,

I am a newbie to linux and struggling to find a better way to append a column in a text file.
Here is the file i want to modify: It has 8 columns (and thousands of rows). I want to append the first column by adding "chr" infront of the numbers. Some rows have a string in the first column and I don't want to change them.
1 . miRNA 548816 548893 . + . ACC="MI0002023"; ID="dre-mir-155";
1 . miRNA 1651461 1651541 . + . ACC="MI0002180"; ID="dre-mir-459";
1 . miRNA 23269491 23269603 . - . ACC="MI0004786"; ID="dre-mir-740";
1 . miRNA 27656240 27656327 . + . ACC="MI0002052"; ID="dre-mir-218a-2";
1 . miRNA 34527751 34527843 . + . ACC="MI0004780"; ID="dre-mir-734";
1 . miRNA 40174414 40174523 . + . ACC="MI0010857"; ID="dre-mir-2197";
1 . miRNA 46862496 46862635 . - . ACC="MI0001895"; ID="dre-mir-16b";
1 . miRNA 46862739 46862822 . - . ACC="MI0001891"; ID="dre-mir-15a-1";
1 . miRNA 55355143 55355233 . - . ACC="MI0004765"; ID="dre-mir-722";
2 . miRNA 1085488 1085564 . + . ACC="MI0002181"; ID="dre-mir-460";
2 . miRNA 6031391 6031475 . + . ACC="MI0002000"; ID="dre-mir-137-1";
2 . miRNA 22105590 22105669 . - . ACC="MI0004782"; ID="dre-mir-736";
2 . miRNA 23568780 23568883 . - . ACC="MI0010841"; ID="dre-mir-2190";
2 . miRNA 25338635 25338716 . - . ACC="MI0001966"; ID="dre-mir-124-1";
2 . miRNA 31878456 31878533 . + . ACC="MI0001916"; ID="dre-mir-23a-3";
2 . miRNA 31880346 31880476 . + . ACC="MI0001928"; ID="dre-mir-27a";
2 . miRNA 34798348 34798457 . + . ACC="MI0010847"; ID="dre-mir-2198";
2 . miRNA 44164796 44164904 . - . ACC="MI0001366"; ID="dre-mir-181b-1";
2 . miRNA 57907954 57908073 . - . ACC="MI0001879"; ID="dre-mir-7a-3";


Is there any simple way to change the first column. Any help will be appreciated.

Thanks
# 2  
Old 12-29-2010
Input
Code:
$ cat file
1	.	miRNA	548816	548893	.	+	.	ACC="MI0002023"; ID="dre-mir-155";
1	.	miRNA	1651461	1651541	.	+	.	ACC="MI0002180"; ID="dre-mir-459";
1	.	miRNA	23269491	23269603	.	-	.	ACC="MI0004786"; ID="dre-mir-740";
1	.	miRNA	27656240	27656327	.	+	.	ACC="MI0002052"; ID="dre-mir-218a-2";
1	.	miRNA	34527751	34527843	.	+	.	ACC="MI0004780"; ID="dre-mir-734";
1	.	miRNA	40174414	40174523	.	+	.	ACC="MI0010857"; ID="dre-mir-2197";
1	.	miRNA	46862496	46862635	.	-	.	ACC="MI0001895"; ID="dre-mir-16b";
str .	miRNA	46862739	46862822	.	-	.	ACC="MI0001891"; ID="dre-mir-15a-1";
1	.	miRNA	55355143	55355233	.	-	.	ACC="MI0004765"; ID="dre-mir-722";
2	.	miRNA	1085488	1085564	.	+	.	ACC="MI0002181"; ID="dre-mir-460";
2	.	miRNA	6031391	6031475	.	+	.	ACC="MI0002000"; ID="dre-mir-137-1";
str .	miRNA	22105590	22105669	.	-	.	ACC="MI0004782"; ID="dre-mir-736";
2	.	miRNA	23568780	23568883	.	-	.	ACC="MI0010841"; ID="dre-mir-2190";
2	.	miRNA	25338635	25338716	.	-	.	ACC="MI0001966"; ID="dre-mir-124-1";
2	.	miRNA	31878456	31878533	.	+	.	ACC="MI0001916"; ID="dre-mir-23a-3";
2	.	miRNA	31880346	31880476	.	+	.	ACC="MI0001928"; ID="dre-mir-27a";
2	.	miRNA	34798348	34798457	.	+	.	ACC="MI0010847"; ID="dre-mir-2198";
2	.	miRNA	44164796	44164904	.	-	.	ACC="MI0001366"; ID="dre-mir-181b-1";
2	.	miRNA	57907954	57908073	.	-	.	ACC="MI0001879"; ID="dre-mir-7a-3";

Command
Code:
sed 's/^\([0-9].*\)/char \1/g' file

Output
Code:
char 1	.	miRNA	548816	548893	.	+	.	ACC="MI0002023"; ID="dre-mir-155";
char 1	.	miRNA	1651461	1651541	.	+	.	ACC="MI0002180"; ID="dre-mir-459";
char 1	.	miRNA	23269491	23269603	.	-	.	ACC="MI0004786"; ID="dre-mir-740";
char 1	.	miRNA	27656240	27656327	.	+	.	ACC="MI0002052"; ID="dre-mir-218a-2";
char 1	.	miRNA	34527751	34527843	.	+	.	ACC="MI0004780"; ID="dre-mir-734";
char 1	.	miRNA	40174414	40174523	.	+	.	ACC="MI0010857"; ID="dre-mir-2197";
char 1	.	miRNA	46862496	46862635	.	-	.	ACC="MI0001895"; ID="dre-mir-16b";
str .	miRNA	46862739	46862822	.	-	.	ACC="MI0001891"; ID="dre-mir-15a-1";
char 1	.	miRNA	55355143	55355233	.	-	.	ACC="MI0004765"; ID="dre-mir-722";
char 2	.	miRNA	1085488	1085564	.	+	.	ACC="MI0002181"; ID="dre-mir-460";
char 2	.	miRNA	6031391	6031475	.	+	.	ACC="MI0002000"; ID="dre-mir-137-1";
str .	miRNA	22105590	22105669	.	-	.	ACC="MI0004782"; ID="dre-mir-736";
char 2	.	miRNA	23568780	23568883	.	-	.	ACC="MI0010841"; ID="dre-mir-2190";
char 2	.	miRNA	25338635	25338716	.	-	.	ACC="MI0001966"; ID="dre-mir-124-1";
char 2	.	miRNA	31878456	31878533	.	+	.	ACC="MI0001916"; ID="dre-mir-23a-3";
char 2	.	miRNA	31880346	31880476	.	+	.	ACC="MI0001928"; ID="dre-mir-27a";
char 2	.	miRNA	34798348	34798457	.	+	.	ACC="MI0010847"; ID="dre-mir-2198";
char 2	.	miRNA	44164796	44164904	.	-	.	ACC="MI0001366"; ID="dre-mir-181b-1";
char 2	.	miRNA	57907954	57908073	.	-	.	ACC="MI0001879"; ID="dre-mir-7a-3";

See in the output, the starting string 'str' doesn't replaced with 'char'
R0H0N
# 3  
Old 12-29-2010
thank you, rohon

It works perfectly.

Thank you,
# 4  
Old 01-03-2011
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
# 5  
Old 01-03-2011
Question should be a separate request

After re-reading your follow-up, this should be its own question. Also, you refer to this as a csv file, but your sample did not seem to be a comma-separated file. It looks like a tab-delimited file.

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