You can change -c and -t parameters on cd-hit that control the identity threshold and redundancy tolerance.

More info: http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide

Trinity FASTA entry example:

>TRINITY_DN1000|c115_g5_i1 len=247 path=[31015:0-148 23018:149-246]
  

AATCTTTTTTGGTATTGGCAGTACTGTGCTCTGGGTAGTGATTAGGGCAAAAGAAGACAC ACAATAAAGAACCAGGTGTTAGACGTCAGCAAGTCAAGGCCTTGGTTCTCAGCAGACAGA AGACAGCCCTTCTCAATCCTCATCCCTTCCCTGAACAGACATGTCTTCTGCAAGCTTCTC CAAGTCAGTTGTTCACAGGAACATCATCAGAATAAATTTGAAATTATGATTAGTATCTGA TAAAGCA

Description of Trinity headers: 'TRINITY_DN1000|c115_g5' corresponds to

'gene id: TRINITY_DN1000|c115_g5' encoding 'isoform id: TRINITY_DN1000|c115_g5_i1'.

I prefer single line FASTA, borrowed from answer on this post:

awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < Trinity.fasta > Trinity_single.fasta

Here's a python script to get the longest isoform per gene:

#!/usr/bin/env python

import sys
from collections import defaultdict

transcripts = defaultdict(list)
with open(sys.argv[1], 'r') as f:
     for line in f:
        if line.startswith(">"):
            transcripts['_'.join(line.strip().split(' ')[0].split('|')[1].split('_')[:2])].append(next(f).strip())  # Groups isoforms by gene id

with open(sys.argv[1].split(".fasta")[1], 'w') as out:
    for t in transcripts:
        print >> out, '>' + t, max(transcripts[t], key=len)

Save as get_longest_iso.py, run as python get_longest_iso.py Trinity_single.fasta