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Help with merge data with a reference sequence

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Top Forums Shell Programming and Scripting Help with merge data with a reference sequence
# 29  
Old 07-31-2016
Could you please answer the question in post #26 ?

----
The post#16 on one (too long) line:
Code:
awk 'NR==FNR {R[$1,$2]=$3; next} FNR>1 {h=$1; len=length($2); print RS h; for(i=2; i<=NF; i++) {s=x; for(j=1; j<=len; j++) {pos=j+(i-2)*len; s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1))}print s}}' FS='\t' file2 FS=" " RS=\> file1

This User Gave Thanks to Scrutinizer For This Post:
cpp_beginner
# 30  
Old 07-31-2016
Hi Scrutinizer,

I run your awk command at terminal as below:
Code:
awk ' NR==FNR { R[$1,$2]=$3 next } FNR>1 { h=$1 len=length($2) print RS h for(i=2; i<=NF; i++) { s=x for(j=1; j<=len; j++) { pos=j+(i-2)*len s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1)) } print s } } ' File_2 RS=\> File_1 > Desired_Output_File
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { h=$1 len=length($2) print RS h for(i=2; i<=NF; i++) { s=x for(j=1; j<=len; j++) { pos=j+(i-2)*len s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1)) } print s } }
awk:                        ^ syntax error
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { h=$1 len=length($2) print RS h for(i=2; i<=NF; i++) { s=x for(j=1; j<=len; j++) { pos=j+(i-2)*len s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1)) } print s } }
awk:                                               ^ syntax error
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { h=$1 len=length($2) print RS h for(i=2; i<=NF; i++) { s=x for(j=1; j<=len; j++) { pos=j+(i-2)*len s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1)) } print s } }
awk:                                                           ^ syntax error
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { h=$1 len=length($2) print RS h for(i=2; i<=NF; i++) { s=x for(j=1; j<=len; j++) { pos=j+(i-2)*len s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1)) } print s } }
awk:                                                                      ^ syntax error
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { h=$1 len=length($2) print RS h for(i=2; i<=NF; i++) { s=x for(j=1; j<=len; j++) { pos=j+(i-2)*len s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1)) } print s } }
awk:                                                                                         ^ syntax error
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { h=$1 len=length($2) print RS h for(i=2; i<=NF; i++) { s=x for(j=1; j<=len; j++) { pos=j+(i-2)*len s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1)) } print s } }
awk:                                                                                                 ^ syntax error
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { h=$1 len=length($2) print RS h for(i=2; i<=NF; i++) { s=x for(j=1; j<=len; j++) { pos=j+(i-2)*len s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1)) } print s } }
awk:                                                                                                                                          ^ syntax error

I believe is I missing some semicolon Smilie
Thanks for advice.
# 31  
Old 07-31-2016
Post #26 was about putting it in a file and running it then. Anyway I also posted the long "one liner version" of post #16 in post #29.
This User Gave Thanks to Scrutinizer For This Post:
cpp_beginner
# 32  
Old 07-31-2016
Hi Scrutinizer,

It seems worked perfectly now Smilie
Let me manual checking it one by one now.

Thanks a lot and again.

---------- Post updated at 11:57 AM ---------- Previous update was at 11:27 AM ----------

Thanks, Scrutinizer.
It worked perfectly after I manual check the output result just now Smilie

Really many thanks for your assist.
Thanks again.
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