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More efficient awk parser

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# 8  
Old 03-13-2015
Definitely not. There's a single quote too many.
Where does the NC last field come from?
# 9  
Old 03-13-2015
loose the ' following FNR > 1
Code:
awk -F'[_.>]' 'FNR > 1 {a=length($4);b=substr($4,1,a-1);print $2+0,b,b,substr($4,a),$5}' OFS='\t' ${id}.txt > ${id}_parse.txt

# 10  
Old 03-13-2015
My guess is that it parses out the NC_004004.4 incorectly. If I use a file with just the variants in it (no header) it works fine. The problem is that the input has a header normally that needs to be skipped. I thought I had it or was close, but it errors and I'm not that good at debugging yet. Thank you Smilie.

Code:
 
awk -F"[_.>]" '{a=length($4);b=substr($4,1,a-1);print $2+0,b,b,substr($4,a),$5}' OFS="\t" Test.txt > output.txt

Test.txt (82 Bytes) 
# 11  
Old 03-13-2015
I attached the output of the command, which runs, but doesn't look right. Thank you Smilie.

Code:
 awk -F'[_.>]' 'FNR > 1 {a=length($4);b=substr($4,1,a-1);print $2+0,b,b,substr($4,a),$5}' OFS='\t' ${id}.txt > ${id}_parse.txt

Code:
 Desired Output
13 20763477 20763477 C T
4 41749507 41749507 G T
4 41749410 41749410 C T

Target.txt (345 Bytes) 
Target_parse.txt (63 Bytes) 
# 12  
Old 03-13-2015
Try
Code:
awk -F"[_.>]" '{X=$4+0; sub(X, "", $4); print $2+0, X, X, $4, $5}' OFS="\t" /tmp/Test.txt 
13      20763477        20763477        C       T
4       41749507        41749507        G       T
4       41749410        41749410        C       T

awk -F"[_.>\t]" 'FNR>1 {X=$4+0; sub(X, "", $4); print $2+0, X, X, $4, $5}' OFS="\t" /tmp/Target.txt 
4004    244     244     G       A
3924    288     288     C       A
3924    385     385     G       A

# 13  
Old 03-14-2015
The output of the second awk skips the header but the first awk has the desired output.

The input will change each time so to represent this ${id}_position.txt is used. An example of the input file is attached. I tried:

Code:
 awk -F"[_.>]" 'FNR > 1 {X=$4+0; sub(X, "", $4); print $2+0, X, X, $4, $5}' OFS="\t" ${id}_position.txt > ${id}_parse.txt

but that didn't work.

Output of script
Code:
 4004	79	79	G	A		NC

Desired Output
Code:
 13     20763642     20763642     C     T

Thank you very much and have a nice weekendSmilie.
GJB-1_position.txt (198 Bytes) 
# 14  
Old 03-14-2015
I modified the code a bit and it works perfectly Smilie thank you for your help.


Code:
 awk 'NR==2 {split($2,a,"[_.>]");b=substr(a[4],1,length(a[4]-1));print a[2]+0,b,b,substr(a[4],length(a[4])),a[5]}' OFS="\t" ${id}_position.txt > ${id}_parse.txt


As you mentioned in a post what if a > is not present, then how to parse. I am encountering that more now, but will post in a new thread. Thank you Smilie
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