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Extract string between two special characters

 
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# 1  
Old 01-24-2015
Extract string between two special characters
Hi,

I have a file that looks something like

Code:
 >1-18*anc
caggttcagctggtgcagtctggagctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggcttctggttacacctttaccagctatggtatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggatggatcagcgcttacaatggtaacacaaactatgcacagaagctccagggcagagtcaccatgaccacagacacatccacgagcacagcctacatggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga
>1-2*anc
caggtgcagctggtgcagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggcttctggatacaccttcaccggctactatatgcactgggtgcgacaggcccctggacaagggcttgagtggatgggacggatcaaccctaacagtggtggcacaaactatgcacagaagtttcagggcagggtcaccatgaccagggacacgtccatcagcacagcctacatggagctgagcaggctgagatctgacgacacggtcgtgtattactgtgcgagaga
>1-24*anc
caggtccagctggtacagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttccggatacaccctcactgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaagatggtgaaacaatctacgcacagaagttccagggcagagtcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaacaga

For each line in the file I'd like to extract the numbers so that I get

Code:
1-18
1-2
1-24

Additionally, I would like to loop through each line of the output. How should I go about these two tasks? Thanks!
# 2  
Old 01-24-2015
The following awk command seems to do what you want for the 1st part:
Code:
awk -F'[>*]' 'NF == 3{print $2}' file

which, with your sample input, produces the output:
Code:
1-18
1-2
1-24

If you want to try this on a Solaris/SunOS system, change awk to /usr/xpg4/bin/awk, /usr/xpg6/bin/awk, or nawk.

What do you mean by: "Additionally, I would like to loop through each line of the output."? Is there some post-processing you want to do to awk's output? Is it something that you can't do in awk?
# 3  
Old 01-24-2015
Another method is to use > as a record separator (which it is) and an asterisk as the field separator.
Code:
awk 'NF{print $1}' FS=\* RS=\> file

or
Code:
awk '{$0=$1}NF' FS=\* RS=\> file

# 4  
Old 01-24-2015
I suppose I'm asking if I have a bash function called foo(), how do I call foo() on every element after the first step of filtering all strings between > and *. Thanks!
# 5  
Old 01-24-2015
Try:
Code:
awk 'NF{print $1}' FS=\* RS=\> file |
while read num
do
  foo "$num"
done


--
You could also do it like this:
Code:
grep -F \> file | 
while IFS='>*' read x num x
do
  foo "$num"
done

Last edited by Scrutinizer; 01-24-2015 at 03:27 AM..
# 6  
Old 01-24-2015
Thank you!
# 7  
Old 01-24-2015
Manually longhand, builtins only, OSX 10.7.5...
Code:
Last login: Sat Jan 24 07:36:07 on ttys000
AMIGA:barrywalker~> IFS=" >*"
AMIGA:barrywalker~> echo ' >1-18*anc
> caggttcagctggtgcagtctggagctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggcttctggttacacctttaccagctatggtatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggatggatcagcgcttacaatggtaacacaaactatgcacagaagctccagggcagagtcaccatgaccacagacacatccacgagcacagcctacatggagctgaggagcctgagatctgacgacacggccgtgtattactgtgcgagaga
> >1-2*anc
> caggtgcagctggtgcagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggcttctggatacaccttcaccggctactatatgcactgggtgcgacaggcccctggacaagggcttgagtggatgggacggatcaaccctaacagtggtggcacaaactatgcacagaagtttcagggcagggtcaccatgaccagggacacgtccatcagcacagcctacatggagctgagcaggctgagatctgacgacacggtcgtgtattactgtgcgagaga
> >1-24*anc
> caggtccagctggtacagtctggggctgaggtgaagaagcctggggcctcagtgaaggtctcctgcaaggtttccggatacaccctcactgaattatccatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaagatggtgaaacaatctacgcacagaagttccagggcagagtcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaacaga' > /tmp/textfile
AMIGA:barrywalker~> text=($(cat /tmp/textfile))
AMIGA:barrywalker~> echo "${text[1]}"
1-18
AMIGA:barrywalker~> echo "${text[3]}"
1-2
AMIGA:barrywalker~> echo "${text[5]}"
1-24
AMIGA:barrywalker~> IFS=$' \t\n'
AMIGA:barrywalker~> _

 
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