fasta file のparser snipet ref: http://qiita.com/yk-tanigawa/items/0361b029863fa17e7ed9

file0.txt

from itertools import groupby
import gzip

# Fasta IO
def fasta_iter(fasta_name):
    '''
    given a fasta file. yield tuples of header, sequence
    modified from Brent Pedersen
    Correct Way To Parse A Fasta File In Python
    https://www.biostars.org/p/710/
    '''

    if((fasta_name[-3:] == '.gz') or 
       (fasta_name[-5:] == '.gzip')):
        with gzip.open(fasta_name, 'rb') as f:
            data = (x[1] for x in groupby(f, lambda line: line.decode('utf-8')[0] == ">"))
            for header in data:
                header = header.__next__().decode('utf-8')[1:].strip()
                seq = "".join(s.decode('utf-8').strip() for s in data.__next__())
                yield(header, seq)
    else:
        with open(fasta_name) as f:
            # ditch the boolean (x[0]) and just keep the header or sequence since
            # we know they alternate.
            data = (x[1] for x in groupby(f, lambda line: line[0] == ">"))
            for header in data:
                # drop the ">"
                header = header.__next__()[1:].strip()
                # join all sequence lines to one.
                seq = "".join(s.strip() for s in data.__next__())
                yield(header, seq)

file1.txt

fasta = '/somewhere/hg19.fa.gz'

seqs = {}
for (head, seq) in fasta_iter(fasta):
    seqs[head] = seq

print(seqs)