UniqueSeqs.py

#from pprint import pprint

FN ='Trinity.fasta'


def get_data(fn):
    with open(fn, mode='r') as fh:
        header, fasta = "",""
        for line in fh:
            if line[0]=='>' and header:
                yield header, fasta
                header = line.strip()
                fasta = ''
            elif line[0]=='>':
                header = line.strip()
            else:
                fasta += line.strip()
        if header:
            yield header, fasta


seqs = {}
for h,f in get_data(FN):
    if h not in seqs or len(f)>len(seqs[h]):
        seqs[h]=f
#pprint(seqs)

def new_fasta(x):
	new_file = open(raw_input('Enter new file name: '), 'a')
	y = x.replace(': ', '\n')
	z = y.strip()
	w = z.replace("', '",'\n')
	q = w.replace("'",'')
	new_file.write(q.strip())

x=str(seqs)
new_fasta(x)