"""
# standard library
import cStringIO
# biopython
from Bio.Blast import NCBIWWW
from Bio import Fasta
# first get the sequence we want to parse from a FASTA file
file_for_blast = open('m_cold.fasta', 'r')
f_iterator = Fasta.Iterator(file_for_blast)
f_record = f_iterator.next()
print 'Doing the BLAST and retrieving the results...'
result_handle = NCBIWWW.blast('blastn', 'nr', f_record)
# save the results for later, in case we want to look at it
save_file = open('m_cold_blast.out', 'w')
blast_results = result_handle.read()
save_file.write(blast_results)
save_file.close()
print 'Parsing the results and extracting info...'
b_parser = NCBIWWW.BlastParser()
# option 1 -- parse the string directly
# b_record = b_parser.parse_str(blast_results)
# option 2 -- create a handle from the string and parse it
string_result_handle = cStringIO.StringIO(blast_results)
