Change names of all sequences in a MSA

Question

[jbt38]

I have a multiple sequence alignment where the names for each sequences are as follows

>gi|AF266048.1|taxonid|126164|organism|Macromia splendens|seqid|AF266048.1|description|Macromia splendens small subunit ribosomal RNA gene partial sequence; mitochondrial gene for mitochondrial product

What I'd like is to have >Macromia_splendens. I'm not sure how to change this for the entire file.

Answer 1

[lieven.sterck]

have a look at some basic linux command line tools, with special focus on sed I would say