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Match patterns from another file and tag

 
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# 1  
Old 01-05-2015
Match patterns from another file and tag
Hi all,

I have a file , which has 6 tab delimited fields, with $3 and $4 subfielded with spaces. I wamt to match cols $2,$3,$4 of tmp1 with tmp2, ..and then flag the 5th col if found.

tmp1
Code:
1756    Xerm    XermA XermB XermC XermD AA TT AA GG     A       1
1763    Xerm    XermA XermB XermC XermD AA TT AA GG     A       1
18078   Xerm    XermA XermB XermC XermD AA TT AA GG     A       1
18115   Xerm    XermA XermB XermC XermD GG AA AA GG     B       2
18251   Xerm    XermA XermB XermC XermD GG AA AA GG     B       2
19352-005       Xerm    XermA XermB XermC XermD AA TT AA GG     A       1
19352-006       Xerm    XermA XermB XermC XermD AA TT AA GG     A       1
195A    Xerm    XermA XermB XermC XermD AA TT AA GG     A       1
A02     Xerm    XermA XermB XermC XermD GG TT GG GG     C       3
A04     Xerm    XermA XermB XermC XermD GG TT AA GG     D       4

tmp2

Code:
Xerm    XermA XermB XermC XermD AA TT AA GG



Expected output

Code:
1756    Xerm    XermA XermB XermC XermD AA TT AA GG     *A*       1
1763    Xerm    XermA XermB XermC XermD AA TT AA GG     *A*       1
18078   Xerm    XermA XermB XermC XermD AA TT AA GG     *A*       1
18115   Xerm    XermA XermB XermC XermD GG AA AA GG     B       2
18251   Xerm    XermA XermB XermC XermD GG AA AA GG     B       2
19352-005       Xerm    XermA XermB XermC XermD AA TT AA GG     *A*       1
19352-006       Xerm    XermA XermB XermC XermD AA TT AA GG     *A*      1
195A    Xerm    XermA XermB XermC XermD AA TT AA GG     *A*       1
A02     Xerm    XermA XermB XermC XermD GG TT GG GG     C       3
A04     Xerm    XermA XermB XermC XermD GG TT AA GG     D       4


Here is what I tried, not producing desired output

Code:
awk -F'\t' 'NR==FNR{a[$0]=$0;next} $2"\t"$3"\t"$4 in a {$5="*"$5"*"}1' OFS="\t"  tmp2 tmp1

# 2  
Old 01-05-2015
Do you really have <TAB> delimiters in both files? For your one line tmp2 file try
Code:
awk     'FNR == NR              {P=$0; next}
         P == $2"\t"$3"\t"$4    {$5="*"$5"*"}
         1
        ' FS="\t" OFS="\t" file2 file1

This User Gave Thanks to RudiC For This Post:
senhia83
# 3  
Old 01-05-2015
Thanks Rudy, you are right.. there are some space and tab issues with tmp2 original file... to get around this is there a way to match the strings without spaces and tabs?
# 4  
Old 01-05-2015
With spaces inside your fields there's no chance to have spaces as delimiters and tell one field from the other reliably. What you could do is replace all whitespace in tmp2 by a regex that would allow you to match the relevant data in tmp1. Try
Code:
awk     'FNR == NR              {gsub (/[ \t]+/, "[ \t]+"); P=$0; next}              
        $2"\t"$3"\t"$4 ~ P      {$5="*"$5"*"}
         1
        ' FS="\t" OFS="\t" file2 file1

If you have multiple lines in tmp2 and read that file into an array a, you need to run a for (i in a) loop and check matches in that loop.
This User Gave Thanks to RudiC For This Post:
senhia83
 
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