I’m on my phone but will try to code it out in Python:

from Bio.SeqIO.FastaIO import SimpleFastaParser
import pandas as pd

with open(path_input, “r”) as f:
    d = dict()
    for id, seq in SimpleFastaParser(f):
        d[id] = seq 
    sequences = pd.Series(d)

lengths = sequences.map(len)

index = lengths.groupby(lambda x: x.split(“_”)[-2]).idxmax()

longest_isoforms = sequences[index]

with open(path_output, "w") as f:
    for id, seq in longest_isoforms.items():
         print(">{}\n{}".format(id,seq), file=f)

Sorry for the autocorrects and formatting. Hope this helps. I’ll clean it up and test later but wanted to answer before I forget.

Edit: Cleaned up the code this morning. Let me know if you have any questions.

Dependencies are pandas and biopython which are pretty standard. This assumes you're ok w/ Python.