CODEWITHSUNDEEP
bashawksedgsubfasta
Babi
Babi

Reputation: 33

Change header of fasta file with sequential numbers

How to change with awk/sed/grep the header of more fasta sequences in a file like:

>chromosome1|2199-2200
----------------------

>chromosome1|3546-3548
----------------------

>chromosome1|6489-6548
----------------------

to this:

>chromosome1-1|2199-2200
------------------------

>chromosome1-2|3546-3548
------------------------

>chromosome1-3|6489-6548
------------------------

At the moment I just can add a sequential number at the beginning or end of the name like:

awk '/^>/{gsub(/^>/,">Seq"i++" ");}1' 

>Seq1chromosome1|2199-2200

Upvotes: 1

Views: 1382

Answers (1)

Ed Morton
Ed Morton

Reputation: 203368

$ awk '/>/{sub(/\|/,"-"++i"|")}1' file
>chromosome1-1|2199-2200
----------------------

>chromosome1-2|3546-3548
----------------------

>chromosome1-3|6489-6548
----------------------

Upvotes: 2

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