If you now that the part you want to delete starts with "|", you can use sed in the terminal:

sed 's/|.*$//' file.fasta > new_file.fasta

What you are doing is to delete all the characters from "|" to the end of the line.

I hope this helps

Hello,

Not a perl answer, but you can do it with the 'gawk' command (or 'awk' if you don't have gawk)

If the separator is only the pipe character, you can do the following:

gawk 'BEGIN{FS="|"}{print $1}' reads.fa

cut -f1 -d "|" input > output

Because I think perl is a terrible language, here's how to do it with biopython:

#!/usr/bin/env python
from Bio import SeqIO
import re

of = open("foobar.fa", "w")
for record in SeqIO.parse("foo.fa", "fasta") :
    matches = re.search("(ENSG[\d]+)", record.id)
    if(matches != None) :
        record.id = matches.group(1);
        record.description=""
    SeqIO.write(record, of, "fasta")
of.close()

You could easily translate that to either perl or bioperl. You could also do this with a sed or awk one-liner.