Finding similar strings between two files


 
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# 1  
Old 04-09-2013
Finding similar strings between two files

Hi,
I have a file1 like this:
Code:
ABAT
ABCA1
ABCC1
ABCC5
ABCC8
ABCE1
ABHD2
ABL1
CAMTA1
ACBD3
ACCN1

And I have a second file like this:
Code:
chr19   46118590        46119564        MACS_peak_1499  3100.00 chr19   46122009        46148405        CYP2B7P1        -2445
chr1    7430312 7430990 MACS_peak_15    2848.88 chr1    6767970 7752353 CAMTA1  678
chr8    129223169       129223828       MACS_peak_3189  2087.99 chr8    129231543       129231616       MIR1208 -7715

I want a script that goes through the 9th column of my second file and find the strings which are similar to my first file and then put an extra string as an extra column at the end of the lines having those similar strings. The extra string should be "estrogen regulated". For example here my output should be a file like this:
Code:
chr19   46118590        46119564        MACS_peak_1499  3100.00 chr19   46122009        46148405        CYP2B7P1        -2445
chr1    7430312 7430990 MACS_peak_15    2848.88 chr1    6767970 7752353 CAMTA1  678         estrogen regulated
chr8    129223169       129223828       MACS_peak_3189  2087.99 chr8    129231543       129231616       MIR1208 -7715

I'm not sure if I could make it clear. Please let me know if you have more questions.
Thanks in advance

Last edited by a_bahreini; 04-09-2013 at 09:03 PM..
# 2  
Old 04-09-2013
You need to explicitly define what "similar" means for this assignment.
# 3  
Old 04-09-2013
I meant exactly the same string. In my example, CMTA1 in the column 9 of the second line in my second file is exactly the same as CMTA1 in my first file. Please let me know if that makes sense to you.
# 4  
Old 04-09-2013
Quote:
Originally Posted by a_bahreini
I meant exactly the same string. In my example, CMTA1 in the column 9 of the second line in my second file is exactly the same as CMTA1 in my first file. Please let me know if that makes sense to you.
It makes sense, but it doesn't match your example. In your example, you have CAMTA1 in column 9 of the second file; but there is no line with that value n the first file. CMTA1 is not the same as CAMTA1.
# 5  
Old 04-09-2013
Oh, I'm sorry. I corrected my post.
# 6  
Old 04-09-2013
OK. I can't really tell from your example, but it looks like you intend to have tabs as field separators. I will assume that the tabs were changed to spaces as part of a copy and paste process. Assuming that it is true, the following should do what you want:
Code:
awk '
FNR == NR {
        a[$1]
        next
}
$9 in a {
        $(NF + 1) = "estrogen regulated"
}
1' OFS="\t" file1 file2

As always, if you're using a Solaris/SunOS system, use /usr/xpg4/bin/awk, /usr/xpg6/bin/awk, or nawk instead of awk.
This User Gave Thanks to Don Cragun For This Post:
# 7  
Old 04-09-2013
That worked. Thanks a lot!
 
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