UNIX for Beginners Questions & Answers

Another option to try:

Code:

awk 'NR>1{print $1, length($2)}' FS='\n' RS=\> OFS='\t' file

If - as specified - you want the sequences in id.txt ONLY, amend scrutinizer's proposal like

Code:

awk 'FNR == NR {T[$1]; next} $1 in T {print $1, length($2)}' id.txt FS='\n' RS=\> OFS='\t' unique.fasta
seq1    6
seq2    7

is it possible to print the order as same as id.txt. The command works fine, but the order has been changed. For example, id.txt file listed the headers as follows,

Code:

seq1
seq2

Where as my unique.fasta file has the sequences in the following order,

Code:

>seq2
ATGCTTA
>seq1
GCTAGT

But, the command print seq2 length first followed by seq1 as shown below.

Code:

seq2     7
seq1      6

Therefore, is it possible to keep the order as same as id.txt.

--- Post updated at 09:43 AM ---

Dear singh,
Is it possible to print the order as same as id.txt. The command works fine, but the order has been changed. For example, id.txt file listed the headers as follows,

Code:

seq1
seq2

Whereas, my unique.fasta file has the sequences in the following order,

Code:

>seq2
ATGCTTA
>seq1
GCTAGT

But, the command print seq2 length first followed by seq1 as shown below.

Code:

seq2     7
seq1    6

Therefore, is it possible to keep the order as same as id.txt.

Well, yes, try

Code:

awk '
FNR == NR       {T[$1] = length($2)
                 next
                }
                {print $1, T[$1]
                }
' FS='\n' RS=\> OFS='\t' unique.fasta RS="\n" id.txt

This has been tested for exactly your setup; for larger or more complex data there may be hickups. Give it a try and report back.

Hello dineshkumarsrk,

Could you please try following.

Code:

awk '
FNR==NR{
  if($0~/^>/){
    sub(/^>/,"")
    val=$0;
    next
  }
  a[val]=(a[val]?a[val] OFS:"")length($0)
  next
}
($0 in a){
  print $0,a[$0]
}
'  Input_file  id.txt

Thanks,
R. Singh

Dear rudic
It works perfectly. But, it prints "0" at last column.
Though it is not a issue at all, but I am reporting the same for your reference.

--- Post updated at 11:52 AM ---

Dear Singh,
It works perfectly fine.

Surprising. This is what I get from your sample data:

Code:

seq1    6
seq2    7

Please show your results...