replace headers in a fasta file

Question

[nicolas.dussex]

Hi,

I would like to replace the first filed my headers in my fasta file and concatenate it to the 2nd field (my gene ID), such a, I start with this:

> maker-scaffold_0-snap-gene-0.23-mRNA-1 gene=maker-scaffold_0-snap-gene-0.23
ATGGTGAAGCTCGTGGCGTTCTCGCCGTTCCGCTCGGCGCAGAGCGCGCTGGAGAACATGAACGCCGTGT
CCGAGGGGGTCCTGCACGAGGACCTGCGGCTGCTGCTGGACACGGCGCTGCCCCCCAAGAGGAA....

and get this:

>Species1_gene=maker-scaffold_0-snap-gene-0.23
ATGGTGAAGCTCGTGGCGTTCTCGCCGTTCCGCTCGGCGCAGAGCGCGCTGGAGAACATGAACGCCGTGT
CCGAGGGGGTCCTGCACGAGGACCTGCGGCTGCTGCTGGACACGGCGCTGCCCCCCAAGAGGAA....

I tried this:

awk ' { $2="Species1_" $2; print }

but it adds Species 1 at the end of each line including the sequence. I assume I shouldn't be too complicated but don't seem to find the solution.

Thanks a lot!

Answer 1

[venu]

If you have maker-scaffold_0-snap-gene-0.23-mRNA-1 -> this part same in all the headers, you can do the following or else you can modify the part after first slash according to your requirements.

perl -pe 's/maker-scaffold_0-snap-gene-0.23-mRNA-1 /Species_1/g' file.fa > modified_file.fa