def main():
time.sleep(1)
Entrez.email = "*****@*****.**"
path = askingforfiles()
X = makedirectory(path.D)
os.chdir(X)
input_GI = get_it(path.I)
blasting = blastin(input_GI)
parser = NCBIWWW.BlastParser()
record = parser.parse(blasting)
with open("blast_results.txt", 'w') as fun:
fun.write(record)
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.qblast('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)
b_record = b_parser.parse(string_result_handle)
# now get the alignment info for all e values greater than some threshold
E_VALUE_THRESH = 0.1
for alignment in b_record.alignments:
for hsp in alignment.hsps:
if hsp.expect < E_VALUE_THRESH:
print '****Alignment****'
