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To print certain patterns in a column

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# 1  
Old 08-20-2012
To print certain patterns in a column
Hi,

From my input files, I want to print $1, $2 and only certain pattern in $4 (EC). I use this code but it print all the words in $4
Code:
awk -F"\t" '$4 {print $1,$2,$4}

I just want EC follows by the numbers in $4

The input file as follows:-

Code:
Entry     Entry name    Status     Names
Q01284   2NPD_NEUCR     R        Nitronate monooxygenase (EC 1.13.12.16) (2-nitropropane dioxygenase) (2-NPD) (Nitroalkane oxidase)
Q99VF6   2NPD_STAAN     U        Probable nitronate monooxygenase (EC 1.13.12.16) (Nitroalkane oxidase)
Q9F131   3HBH1_PSEAC    R        3-hydroxybenzoate 6-hydroxylase 1 (EC 1.14.13.24) (Constitutive 3-hydroxybenzoate 6-hydroxylase)
Q5EXK1   3HBH_KLEOX     R        3-hydroxybenzoate 6-hydroxylase (EC 1.14.13.24)
P07046   3SHD_NEUCR     R        3-dehydroshikimate dehydratase (DHS dehydratase) (DHSase) (EC 4.2.1.-)

The output should be:-

Code:
Entry     Entry name         Names
Q01284   2NPD_NEUCR        EC 1.13.12.16
Q99VF6   2NPD_STAAN        EC 1.13.12.16
Q9F131   3HBH1_PSEAC       EC 1.14.13.24
Q5EXK1   3HBH_KLEOX        EC 1.14.13.24
P07046   3SHD_NEUCR        EC 4.2.1.-

Would appreciate your kind help on this. Thanks
Last edited by redse171; 08-20-2012 at 10:37 PM.. Reason: typo
# 2  
Old 08-20-2012
Have a go with this:

Code:
awk -F "\t"  '
    NR == 1 { printf( "%s\t%s\t%s\n", $1, $2, $4 ); next; }
    NR > 1 {
        gsub( ".*EC", "EC", $4 );
        gsub( "\\).*", "", $4 );
        printf( "%s\t%s\t%s\n", $1, $2, $4 );
    }
'  input-file >output-file

Last edited by agama; 08-20-2012 at 10:58 PM.. Reason: oops, header wrong.
This User Gave Thanks to agama For This Post:
redse171
# 3  
Old 08-20-2012
Hi agama,

i tried but it did not change anything. it still print the whole words in $4
# 4  
Old 08-20-2012
What Operating system and version of awk are you using? If you are on Sun/Solaris, try nawk instead of awk.
# 5  
Old 08-20-2012
If you have gawk, please try this:

Code:
awk -F"\t" 'match($0, /(EC [0-9\-\.]+)/, p) { print $1,$2,p[1]}'

This User Gave Thanks to leafei For This Post:
redse171
# 6  
Old 08-20-2012
Hi,

i am using ubuntu 10.04.
# 7  
Old 08-20-2012
What is the output of awk --version

Both the programme that I posted, and that leafei posted generate expected results with awk Version 4.0.0.

Are you sure that your columns are tab separated? If it's not, that would cause my solution to fail; leafei's match() works against the whole record and thus wouldn't be subject to that issue if the file is not tab separated.
This User Gave Thanks to agama For This Post:
redse171
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