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# 1  
Old 11-15-2014
Match and copy
Code:
Trying to match $4 in LCH_exons.txt with $1 in refseq_genes.txt, if there is a match then the value in $4 in refseq_exons is copied to $5 of LCH_exons.

For example, $4 in LCH_exons.txt is NRAS and that matches $1 row 11270 and the value in $4 is -, so the - would be copied to LCH_exons.txt in $5.

Code:
 
chr1	115247084	115250671	NRAS
chr1	115250774	115250813	NRAS
chr1	115251151	115251275	NRAS
chr1	115252189	115252349	NRAS
chr1	115256420	115256599	NRAS
chr1	115258670	115258798	NRAS
chr1	115259278	115259515	NRAS

After the match
Code:
chr1	115247084	115250671	NRAS	-
chr1	115250774	115250813	NRAS	-
chr1	115251151	115251275	NRAS	-
chr1	115252189	115252349	NRAS	-
chr1	115256420	115256599	NRAS	-
chr1	115258670	115258798	NRAS	-
chr1	115259278	115259515	NRAS	-

Is this possible? Thank you Smilie.
match.zip (1.94 MB) 
# 2  
Old 11-15-2014
Please check your sample data, the 1968 lines in LCH_exons.txt is a subset of refseq_exons.txt.
# 3  
Old 11-16-2014
Quote:
Originally Posted by cmccabe
. . . Is this possible? Thank you Smilie.
Almost certainly - provided you get your act together.

Four file names (LCH_exons.txt, refseq_genes.txt, refseq_exons, and LCH_exons) are supplied of which only one matches one in your attached samples, of which, as derekludwig points out, none meets the structure of your second file.

Would you like to receive a proposal of the same quality as the request?
# 4  
Old 11-17-2014
I apologize for the confusion and have attached the proper files.

Code:
Trying to match $4 in LCH_exons.txt with $1 in refseq_genes.txt, if there is a match then the value in $4 in refseq_exons is copied to $5 of LCH_exons.

For example, $4 in LCH_exons.txt is NRAS and that matches $1 row 11270 and the value in $4 is -, so the - would be copied to LCH_exons.txt in $5.

Thank you Smilie.

Maybe:
Code:
 awk 'NR==FNR{A[$1]=$1}A[$5]{sub($5,A[$5]);print}' refseq_genes.txt LCH_exons.txt > output.txt

match.zip (4.66 MB) 
Last edited by cmccabe; 11-17-2014 at 10:26 AM..
# 5  
Old 11-17-2014
That refseq_genes file is pretty big. Anyhow, adapt your script like (untested)
Code:
 awk 'NR==FNR{A[$1]=$4; next}  A[$4]  {$4=$4 " " A[$4]}1' refseq_genes.txt LCH_exons.txt > output.txt

This User Gave Thanks to RudiC For This Post:
cmccabe
# 6  
Old 11-17-2014
I get this error:

Code:
 
awk: cmd. line:1: NR==FNR{A[$1]=$4; next} A[$4] {$4=$4 " " A[$4])}1
awk: cmd. line:1: ^ syntax error

Thank you Smilie.

---------- Post updated at 12:33 PM ---------- Previous update was at 08:46 AM ----------

Never mind, I must have copied an extra space... it works great. Thank you Smilie
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