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awk for string between > and /n

 
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# 1  
Old 03-18-2015
awk for string between > and /n
Hi, I have a file that looks something like the following:

Code:
>IGHV4-4*02
caggtgcagctgcaggagtcgggcccaggactggtgaagccttcggggaccctgtcc
ctcacctgcgctgtctctggtggctccatcagcagtagtaactggtggagt
tgggtccgccagcccccagggaaggggctggagtggattggggaaatctatcatagt
gggagcaccaactacaacccgtccctcaagagtcgagtcaccatatcagta
gacaagtccaagaaccagttctccctgaagctgagctctgtgaccgccgcggacacggcc
gtgtattactgtgcgagaga
>IGHV4-4*03
caggtgcagctgcaggagtcgggcccaggactggtgaagcctccggggaccctgtcc
ctcacctgcgctgtctctggtggctccatcagcagtagtaactggtggagt
tgggtccgccagcccccagggaaggggctggagtggattggggaaatctatcatagt
gggagcaccaactacaacccgtccctcaagagtcgagtcaccatatcagta
gacaagtccaagaaccagttctccctgaagctgagctctgtgaccgccgcggacacggcc
gtgtattactg
>IGHV4-4*04
caggtgcagctgcaggagtcgggcccaggactggtgaagcctccggggaccctgtcc
ctcacctgcgctatctctggtggctccatcagcagtagtaactggtggagt
tgggtccgccagcccccagggaaggggctggagtggattggggaaatctatcatagt
gggagcaccaactacaacccgtccctcaagagtcgagtcaccatatcagta
gacaagtccaagaaccagttctccctgaagctgagctctgtgaccgccgcggacacggcc
gtgtattactg

I would like to use awk to obtain a list [IGHV4-4*02, IGHV4-4*03, IGHV4-4*04]. How do I awk for the string between > and the newline?
# 2  
Old 03-19-2015
Try:
Code:
sed -n 's/^>//p' file

# 3  
Old 03-19-2015
Hello jyu429,

Following may also help you in same.
Code:
awk '/^>/ {print substr($0,2)}'  Input_file

Output will be as follows.
Code:
IGHV4-4*02
IGHV4-4*03
IGHV4-4*04

Thanks,
R. Singh
# 4  
Old 03-19-2015
This question is pretty similar to the other four requests you have made to have us write code for you. When you ask for help in the future, please show us what you have tried to solve your problem.

Try something like:
Code:
awk -F'>' 'NF > 1 {printf("%s%s", cnt++ ? ", " : "[", $2)} END {print "]"}' file

which, with your sample input, produces the output:
Code:
[IGHV4-4*02, IGHV4-4*03, IGHV4-4*04]

which seems to match the output you wanted.

If you want to try this on a Solaris/SunOS system, change awk to /usr/xpg4/bin/awk.
 
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