Duplicate fasta header and append it with a pipe

Question

[bionix]

Hello All,

I have a multi fasta file with millions of sequences. I want to duplicate a part of the header and join it to the header itself with a pipe, while another part (of the header) should be deleted.

Let's say I have a fasta file, "input.fasta," which looks like this:

>Gene1 wbdfwbf
ATGCCGATGCAGTGACG
>Gene2 wbdwe
ATGCAGTGACGTAGCAG
>Gene3 wdbwd
TGACGTAGCGTAGCAG

I want it to convert to:

>Gene1|Gene1
ATGCCGATGCAGTGACG
>Gene2|Gene2
ATGCAGTGACGTAGCAG
>Gene3|Gene3
TGACGTAGCGTAGCAG

First, I used cut -d ' ' -f 1 < input.fasta > out1.fasta for deleting space followed by all the characters from the header and then added a pipe by doing perl -p -e 's/^(>.*)$/$1\|/g' out1.fasta > out2.fasta

out2.fasta looks like this:

>Gene1|
ATGCCGATGCAGTGACG
>Gene2|
ATGCAGTGACGTAGCAG
>Gene3|
TGACGTAGCGTAGCAG

Now I am stuck here. I have come across many posts on deleting duplicates on the forum but didn't see any post on duplicating fasta header. Could you please help me with this or point out a solution if it has already been discussed?

Many Thanks, PSP

Answer 1

[Pierre Lindenbaum]

sed  '/^>/s/>\([^ ]*\).*/>\1|\1/'  in.fa

[bionix]

Thank you very much!