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Grepping one file column from another file

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# 1  
Old 12-26-2013
Grepping one file column from another file
Hi all,

I want to search the second col of a file as a sub-part of 4th col of another file and produce a joint output. In the example, search if B is contained as a sub-part in E:B:C (sub-parts separated by colons). Note the second row is not found doesnt find a match as F isnt there in col 4 second file (second line).

Code:
file1

A B
E F
G H

file2
C D L E:B:C  
Z Y F FFFF:EEE:PP
G H R H:H:I:J

out

A B C D L E:B:C  
E F
G H G H R H:H:I:J

Here is what I tried but doesn't work

Code:
awk ' NR == FNR { y[":"$2":"] next  }{ x = ":"$4":" for (i in y)  if (index(x,i)) print i, $0 } file1 file2

# 2  
Old 12-26-2013
Try this:
Code:
awk '
        NR == FNR {
                A[$0] = $NF
                next
        }
        {
                for ( k in A )
                {
                        n = split ( A[k], R, ":" )
                        for ( i = 1; i <= n; i++ )
                        {
                                if ( R[i] == $2 )
                                {
                                        print $0, k
                                        f = 1
                                        break
                                }
                        }
                }
                if ( !(f) )
                        print $0
                f = 0
        }
' file2 file1

This User Gave Thanks to Yoda For This Post:
newbie83
# 3  
Old 12-26-2013
Another approach :
Code:
$ awk  'FNR==NR{A[$4]=$0;next}{x=0;for(i in A){split(A[i],X,":");if($2==X[2]){x=1;print $0,A[i]}}if(x==0)print}'  file2 file1
A B C D L E:B:C  
E F
G H G H R H:H:I:J

Last edited by Akshay Hegde; 12-26-2013 at 01:55 PM..
This User Gave Thanks to Akshay Hegde For This Post:
newbie83
# 4  
Old 12-26-2013
is it possible to limit the search by the first hit? That will reduce the runtime considerably, so as soon as the first hit is met, I would like to move on to the next line in file1, similar to a break in C.
# 5  
Old 12-26-2013
Quote:
Originally Posted by newbie83
is it possible to limit the search by the first hit? That will reduce the runtime considerably, so as soon as the first hit is met, I would like to move on to the next line in file1, similar to a break in C.
Yes, as soon as field2 of file1 == 2nd sub field of field4 of file2 is true print line of file1 and line of file2 and then next, if you use break here it just terminates loop does not move to next line
Code:
$ awk  'FNR==NR{A[$4]=$0;next}{x=0;for(i in A){split(A[i],X,":");if($2==X[2]){x=1;print $0,A[i];next}}if(x==0)print}' file2 file1

Example :
Code:
$ awk  'FNR==NR{A[$4]=$0;next}{x=0;for(i in A){split(A[i],X,":");if($2==X[2]){x=1;print $0,A[i]}}print "without next and break";if(x==0)print}' file2 file1
A B C D L E:B:C  
without next and break
without next and break
E F
G H G H R H:H:I:J
without next and break

$ awk  'FNR==NR{A[$4]=$0;next}{x=0;for(i in A){split(A[i],X,":");if($2==X[2]){x=1;print $0,A[i];next}}print "with next";if(x==0)print}' file2 file1
A B C D L E:B:C  
with next
E F
G H G H R H:H:I:J

$ awk  'FNR==NR{A[$4]=$0;next}{x=0;for(i in A){split(A[i],X,":");if($2==X[2]){x=1;print $0,A[i];break}}print "with break";if(x==0)print}' file2 file1
A B C D L E:B:C  
with break
with break
E F
G H G H R H:H:I:J
with break

Last edited by Akshay Hegde; 12-26-2013 at 03:51 PM..
# 6  
Old 12-26-2013
Can you let me know what I`m doing wrong, this is part of a real data-set where I`m trying to search col2 from file1 in col5 in file2.

File2
Code:
# cat inp2.txt
Q0UR51  Q0UR51_PHANO    5973037 XP_001796160.1  111065707: 169605479            GO:0004190; GO:0006508          UniRef100_Q0UR51        UniRef90_Q0UR51 UniRef50_N4XCZ1 UPI0000DD11E3           321614                  18024570        CH445332     EAT86827.1

Code:
# cat inp1.txt
comp100008_c0_seq1      169605479
comp1001565_c0_seq1     326493850
comp10017_c0_seq1       399172251
comp10020_c0_seq1       322703447
comp100416_c0_seq1      115471291
comp10045_c0_seq1       473789509
comp1007987_c0_seq1     357112415
comp100803_c0_seq1      475610100
comp10090_c0_seq1       322706779
comp1009402_c0_seq1     326510337

Code:
# awk  -F"\t" 'FNR==NR{A[$5]=$0;next}{x=0;for(i in A){split(A[i],X,":");if($2==X[2]){x=1;print $0,A[i];next}}if(x==0)print}' inp2.txt inp1.txt
comp100008_c0_seq1      169605479
comp1001565_c0_seq1     326493850
comp10017_c0_seq1       399172251
comp10020_c0_seq1       322703447
comp100416_c0_seq1      115471291
comp10045_c0_seq1       473789509
comp1007987_c0_seq1     357112415
comp100803_c0_seq1      475610100
comp10090_c0_seq1       322706779
comp1009402_c0_seq1     326510337

# 7  
Old 12-26-2013
Yoda's code will find a match if any subpart of field 4 in file2 is matched by field 2 in file1. Akshay's code will find a match only if the 2nd subpart of field 4 in file 2 is matched by field 2 in file1.

If I read your requirements correctly, I think Yoda's interpretation is what was wanted. The following is an alternative approach that should produce the same output. Depending on the sizes of the input files, this should run faster but use a little more memory:
Code:
awk '
NR == FNR {
        n = split($4, f, /:/)
        for(i = 1; i <= n; i++) o[f[i]] = " " $0
        next
}
{       print $0 o[$2]
}' file2 file1

Note that if there are multiple lines in file2 with with identical subfields in field4, this will print the last match rather than the 1st. If you need the 1st instead of the last match, change:
Code:
        for(i = 1; i <= n; i++) o[f[i]] = " " $0

to:
Code:
        for(i = 1; i <= n; i++) if(!(f[i] in o)) o[f[i]] = " " $0

If you want to try this on a Solaris/SunOS system, use /usr/xpg4/bin/awk, /usr/xpg6/bin/awk, or nawk instead of awk.
These 2 Users Gave Thanks to Don Cragun For This Post:
newbie83 Yoda
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