Awk? Append an incremental number to each line containing a symbol

Question

I have a file of sequences.

>seqA
lakjdsflakjsdlkjals;dkjfal;kdjsfl;aksdjf;lakjsdfl;kjalsdkjf
alsdkjfalskdjf;alsdfj;alkdjsf;lakjsdf;lkajsd
>seqB
fjal;kdjsfla;kdjsflkajdslkjfaghal;sdkjg
>seqC
a;lksdjl;akjsdg;lkjsdfl;kajdsl;kgj;alkdjsg;lkajsdgl
lsdkfja;lksdjf;lakdjsf;lkajsdfl;kjal;sdkfjal;skdjak
sdkjfal;ksdjflk;ahdglkahsdl;kghalk

I'd like to add an increasing incremental number after each ">"

For example:

Output file:

>1seqA
lakjdsflakjsdlkjals;dkjfal;kdjsfl;aksdjf;lakjsdfl;kjalsdkjf
alsdkjfalskdjf;alsdfj;alkdjsf;lakjsdf;lkajsd
>2seqB
fjal;kdjsfla;kdjsflkajdslkjfaghal;sdkjg
>3seqC
a;lksdjl;akjsdg;lkjsdfl;kajdsl;kgj;alkdjsg;lkajsdgl
lsdkfja;lksdjf;lakdjsf;lkajsdfl;kjal;sdkfjal;skdjak
sdkjfal;ksdjflk;ahdglkahsdl;kghalk

So far after scouring the internet I've tried:

awk -F "i=1" '{if (/>/){print $0i++} else print}'

and it didn't do anything. What am I doing wrong?

Thanks!

Answer 1

Try:

awk '/>/{$0 = ">" ++i substr($0, 2)} 1'

For example:

$ awk '/>/{$0 = ">" ++i substr($0, 2)} 1' file
>1seqA
lakjdsflakjsdlkjals;dkjfal;kdjsfl;aksdjf;lakjsdfl;kjalsdkjf
alsdkjfalskdjf;alsdfj;alkdjsf;lakjsdf;lkajsd
>2seqB
fjal;kdjsfla;kdjsflkajdslkjfaghal;sdkjg
>3seqC
a;lksdjl;akjsdg;lkjsdfl;kajdsl;kgj;alkdjsg;lkajsdgl
lsdkfja;lksdjf;lakdjsf;lkajsdfl;kjal;sdkfjal;skdjak
sdkjfal;ksdjflk;ahdglkahsdl;kghalk

How it works

• />/{$0 = ">" ++i substr($0, 2)}

  This selects lines that contain >. For those lines, we replace the line $0 with > followed by ++i (which is the value of the variable i after it has been incremented) followed by the current line starting at its second character.

• 1

  This is awk's shorthand for print-the-line.

Answer 2

You can try

awk '/^>/{sub(/^>/,">"++i)}1' infile