gistfile1.py

import re

#open file to read
with open('test.fasta', 'r') as seqs:

	seqFile = (open('throwaway.txt', 'a+'))

	for line in seqs:
		if re.search('^>[a-zA-Z][a-zA-Z][a-zA-Z][a-zA-Z]', line):
			seqFile.close()
			seqFile = open('%s.fasta' % line, 'a+')
			seqs.next()
		else:
			seqFile.write('%s' % line)

	seqFile.close()

gistfile2.py

import re

#open file to read
with open('test.fasta', 'r') as seqs:

	#seqFile = (open('throwaway.txt', 'a+'))
	mydict = {}

	for line in seqs:
		if re.search('^>[a-zA-Z][a-zA-Z][a-zA-Z][a-zA-Z]', line):
			fileName = line + '.fasta'
			if fileName not in mydict:
				mydict[fileName] = open(fileName, 'a+')
			seqs.next()
		else:
			#seqFile.write('%s' % line)
			mydict[fileName].write('%s' % line)
	seqFile.close()