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My data is like below 

sp|Q9H9K5|MER34_HUMAN(9-21)
sp|Q9H9K5|MER34_HUMAN(493-507)
sp|Q9H9K5|MER34_HUMAN(524-539)
sp|P31689|DNJA1_HUMAN(22-33)
sp|P31689|DNJA1_HUMAN(66-82)
sp|P31689|DNJA1_HUMAN(93-104)
sp|P08246|ELNE_HUMAN(7-27)
sp|P08246|ELNE_HUMAN(72-83)
sp|P10144|GRAB_HUMAN(5-13)

I am trying to extract the string between ||

sed -n " ||" file
grep "||" file

did not work .

desire output is like this 

Q9H9K5
Q9H9K5
Q9H9K5
P31689
P31689
P31689
P08246
P08246
P10144

Then I want to make them unique 

 Q9H9K5
 P31689
 P08246
 P10144
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1
  • It's easy to solve it when you use awk, just two steps Commented Feb 18, 2019 at 17:46

2 Answers 2

Reset to default
3

You can use cut here to nice effect.

cut -d\| -f2 myfile.txt

Produces the following output:

Q9H9K5
Q9H9K5
Q9H9K5
P31689
P31689
P31689
P08246
P08246
P10144

The -d tells cut to look out for the pipe character to delimit the columns of your output (in this case we must escape it). The -f specifies which column (or columns) of your input you want back. Columns are numbered starting with 1.

If you only want the unique values, you can pipe that output into sort and uniq as follows: 

cut -d\| -f2 myfile.txt | sort | uniq

This produces:

P08246
P10144
P31689
Q9H9K5
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3
  • 1
    Alternatively: cut -d '|' -f 2 file | sort -u or with just uniq instead of sort -u if the data is already sorted. Commented Feb 18, 2019 at 17:07
  • You can use sort -u instead of sort|uniq Commented Feb 18, 2019 at 17:09
  • @mttpgn I liked it already Commented Feb 18, 2019 at 17:31
2

You can try something like:

awk -F\| '{print $2}' input_file|sort -u
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4
  • does not make them unique, just sort them Commented Feb 18, 2019 at 16:53
  • @Learner, did you saw the key -u at the end of sort? This is to output only unique values (after sort) Commented Feb 18, 2019 at 16:56
  • 2
    ... or all in awk: awk -F'|' '!seen[$2]++ {print $2}' input_file Commented Feb 18, 2019 at 17:01
  • 1
    @Romeo Ninov I liked it already Commented Feb 18, 2019 at 17:30

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