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Match pattern in a field, print pattern only instead of the entire field

 
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# 8  
Old 03-02-2012
Quote:
Originally Posted by lucasvs
Code:
awk '$2 {gsub(/ /,"");print}' file.tab

awk splits the line into fields based on whitespaces by default. So $2 is not "bb11 toma toes 111b bbbbb" but just "bb11". Tell awk to split fields based on tab '\t' and then $2 would be what you think it is (unless ofcourse, columns are tab separated).

Code:
awk -F'\t' 'BEGIN{OFS="\t"} {gsub(/ /,"",$2); print}' file.tab

This User Gave Thanks to balajesuri For This Post:
lucasvs
# 9  
Old 03-02-2012
Thanks it is very helpful. I understand now.

I notice that this work as well:
Code:
awk -F'\t'  '{gsub(" ","",$6); print $0}' file.tab

---------- Post updated at 02:33 AM ---------- Previous update was at 02:25 AM ----------

About the initial perl command you gave, sometimes I have this error message bout the quantifiers:
Code:
Nested quantifiers in regex; marked by <-- HERE in m/([1-9]?{ <-- HERE 0,10}tomatoes[1-9]?{0-10})/ at -e line 1.

# 10  
Old 03-02-2012
Please post the exact perl one-liner you used.

From the error message, I can only guess that you used something like this: /([1-9]?{0,10}tomatoes[1-9]?{0,10}/.

What did you want to achieve? Why would you give '?' and then define intervals too?

? and {0,10} are both quantifiers.
? refers to zero or one match of the previous character.
{0,10} refers to zero to 10 matches of previous character.

? is a quantifier and so is {0,10}. In your regex, ? is followed by {0,10}, and hence the error message 'Nested quantifiers in regex'
# 11  
Old 03-03-2012
ok !

Actually I just remove the "?" as it is the same than "{0,x}".

I tested the perl command you gave earlier without the "?":
Code:
perl -lane 'if ($F[1] =~ /([13]{1,5}tomatoes[13]{1,5})/) {$F[1] =~ s/.*?($1).*/$1/; print join ("\t", @F)}' file.tab

It works on the example I gave in the post, but returns a blank file when I use it on my real files (the pattern is not in the 3rd but the 6th field).
Is your perl command dependent on the field in which the pattern is?
In other words, do I have to modify it if I want to search the pattern in the 6th field?
# 12  
Old 03-03-2012
If you are using gawk, it does not understand the regex repetition operator by default, even though it is specified in POSIX. Use gawk --posix
# 13  
Old 03-04-2012
* Thanks Scrutinizer !
I get it now.

* About balajesuri's perl command:
Code:
perl -lane 'if ($F[1] =~ /([13]{1,5}tomatoes[13]{1,5})/) {$F[1] =~ s/.*?($1).*/$1/; print join ("\t", @F)}' file.tab

It doesn't work on the following type of file (pattern to search/extract/replace in the 6th field, instead of the 3rd like in the example; total of 8 fields instead of 3 like in the example):
Code:
Field1   Field2   Field3   Field4   Field5   Field6   field7   Field8
A1   A2   A3   A4   A5   bb11tomatoes111bbbbbb   A7   A8
B1   B2   B3   B4   B5   eeee2222apples2eeeeeeeee   B7   B8
C1   C2   C3   C4   C5   hhhhhh33333tomatoes33333hhh   C7   C8

It returns the same entire file (matching and non-matching lines):
Code:
Field1   Field2   Field3   Field4   Field5   Field6   field7   Field8
A1   A2   A3   A4   A5   bb11tomatoes111bbbbbb   A7   A8
B1   B2   B3   B4   B5   eeee2222apples2eeeeeeeee   B7   B8
C1   C2   C3   C4   C5   hhhhhh33333tomatoes33333hhh   C7   C8

I tried, in the command, to divide the pattern into compartments using brackets:
Code:
perl -lane 'if ($F[1] =~ /(([13]{1,5})(tomatoes)([13]{1,5}))/) {$F[1] =~ s/.*?($1).*/$1/; print join ("\t", @F)}' file.tab

,and it returns a blank file.
# 14  
Old 03-04-2012
You are selecting on the sixth column instead of the second column in the example of the starting post, so then you need to replace F[1] with F[5] and are these fields tab separated? Slight modification of balajesuri's code:
Code:
perl -lane 'if ($F[5] =~ s/.*?([13]{1,5}tomatoes[13]{1,5}).*/$1/) {print join ("\t", @F)}' in file

Code:
perl -F\\t -lane 'if ($F[5] =~ s/.*?([13]{1,5}tomatoes[13]{1,5}).*/$1/) {print join ("\t", @F)}' infile

Last edited by Scrutinizer; 03-04-2012 at 10:11 PM..
This User Gave Thanks to Scrutinizer For This Post:
lucasvs
 
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