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Match working for some but not all

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# 1  
Old 06-26-2015
Match working for some but not all
I am not sure why the script below seems to pull the correct values for most, but not all. Basically what is supposed to result is the $1 value in genes.txt is matched to the $3 value in RefSeqGene.txt and the value in 6 field is copied. In the output below that is the case most of the time but not always and I'm not sure why. Thank you Smilie.


Code:
awk 'FNR==NR {E[$1]; next }$3 in E {print $3, $5}' genes.txt RefSeqGene.txt > update.txt

Output:
Code:
AAGAB NM_001271886.1
AANAT NM_001166579.1
AANAT NR_110548.1
AANAT NM_001088.2
AARS LRG_359  (should be NM_001605.2)
ABCC9 LRG_377 (should be NM_005691.2)
ABCC9 LRG_377 (should be NM_020297.2)
ABCC9 LRG_377 (should be NM_005691.3)
ABCC9 LRG_377 (should be NM_020297.3)

files.zip (200.4 KB) 
# 2  
Old 06-26-2015
Why do you print $5 if you want field 6? If you know the answer, you know the cause of the problem.
This User Gave Thanks to RudiC For This Post:
cmccabe
# 3  
Old 06-26-2015
In addition change FS and OFS to \t for the 2nd file...

Code:
awk 'FNR==NR {E[$1]; next }$3 in E {print $3, $6}' genes.txt FS='\t' OFS='\t'  RefSeqGene.txt

Last edited by Scrutinizer; 06-26-2015 at 03:54 PM..
This User Gave Thanks to Scrutinizer For This Post:
cmccabe
# 4  
Old 06-26-2015
I'm not sure why, but before I couldn't get it to work.... maybe I was typing something wrong. Thank you Smilie.
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