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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
# 8  
Old 07-31-2016
Hi,

It seems like no work Smilie
It return the header together with the length of the fasta file I believe.
Code:
awk 'NR==FNR {a[$1,$2]=$2; b[$1,$2]=$3; c[$1]=$1; next} /^>/ {w=$0; sub(".*> *", "", w)} ! /^>/ && c[w] {for (i in a) $(a[i])=b[i]} 1 ' file2 FS= OFS= file1

>Data_1
2421442

Thanks.
# 9  
Old 07-31-2016
Probably this is because of what I mentioned in the note in post #5 about FS=
# 10  
Old 07-31-2016
Hi Scrutinizer,

I try with your awk code. It seems to return "Syntax error" Smilie
Code:
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { s=x for(i=1; i<=length($2); i++) s=s (($1,i) in R ? R[$1,i] : substr($2,i,1)) print RS $1 FS s }
awk:                        ^ syntax error
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { s=x for(i=1; i<=length($2); i++) s=s (($1,i) in R ? R[$1,i] : substr($2,i,1)) print RS $1 FS s }
awk:                                           ^ syntax error
awk:  NR==FNR { R[$1,$2]=$3 next } FNR>1 { s=x for(i=1; i<=length($2); i++) s=s (($1,i) in R ? R[$1,i] : substr($2,i,1)) print RS $1 FS s }
awk:                                                                                                                     ^ syntax error

I just type the below command at my terminal:
Code:
awk ' NR==FNR { R[$1,$2]=$3 next } FNR>1 { s=x for(i=1; i<=length($2); i++) s=s (($1,i) in R ? R[$1,i] : substr($2,i,1)) print RS $1 FS s } ' file2 RS=\> FS='\n' file1

I type it as a long awk command Smilie
My Operation System is "x86_64 x86_64 x86_64 GNU/Linux". My awk is "GNU Awk 3.1.7".

Would it be the main problem cause it return syntax error?
Thanks a lot and again for your advice.

---------- Post updated at 05:01 AM ---------- Previous update was at 05:00 AM ----------

Hi,

I believe so Smilie
Do you have any advice regarding my concern?

Sorry.
Still quite new about awk,perl, etc shell script and programming Smilie
# 11  
Old 07-31-2016
You did not turn it into a one-liner properly, watch the semicolons. Try:
Code:
awk 'NR==FNR{R[$1,$2]=$3; next} FNR>1{s=x; for(i=1; i<=length($2); i++) s=s (($1,i) in R ? R[$1,i] : substr($2,i,1)); print RS $1 FS s}' file2 RS=\> FS='\n' file1

But you do not have to turn it into a one-liner, you can also paste multiple lines or put it in a file and execute that.

---
With your version of awk the other script should work too, probably you forgot to put semicolons there too
# 12  
Old 07-31-2016
Hi Scrutinizer,

Thanks again.
It worked perfectly with my sample sequence provided.
However I aware if I replace it with my real own data set.
It just print out the original File 1 Smilie

Would it the fasta sequence length issue?
My original file is around 2 million word and is single line.

My File 1 is 2 Line; First Line is header description and second line is a very long word (around 2 million).

My File 2 is tab-delimited file.
First column is the header of File 1;
Second column is the word to replace in File 1;
Third column is position of word to replace in File 1;
# 13  
Old 07-31-2016
I think that is too long. The Fasta format allows wrapping of the sequence over multiple lines. That should be an option in the program you used to generate the file with.

Please indicate if you would like to go that route, then I can adjust my suggestion, so that it works for that format as well..
This User Gave Thanks to Scrutinizer For This Post:
cpp_beginner
# 14  
Old 07-31-2016
Many thanks for your help.

I split the long sequence into 100 word a line now.
Unfortunately the output file just return the header with the first 100 word record Smilie
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