That is how my fasta file looks like:
>monCan3F9-B-G1795-Map9 TTTATTATACCCTGAACCCATTAAAA(multiple lines) >monJX13F48-L-B718-Map1 AAAATTAATTCAGAATTATGTTTG(multiple lines) . . .
the list of new names are not in the same order as in the fasta file, so I have to define it like this e.g. :
monCan3F9-B-G1795-Map9 > BARI1#DNA/Tc1-Mariner monJX13F48-L-B718-Map1 > PARIS#LTR . .
for a few names, I could do that manually using 'sed' but I don't know how to do it when I have about 1000 of them! I tried to check samtools manual but as far as I understood it requires sam and bam files, is there any other toolkit to do such a thing?