def blast_remos(r, db='nr'):
"""Uses blast to find remos in a genome"""
from Bio.Blast import NCBIWWW, NCBIXML
import cStringIO
b_parser = NCBIXML.BlastParser()
E_VALUE_THRESH = 0.04
for s in r.get_aligned_sequences():
for remo in r.get_remos_for(s):
seq = remo.get_sequence_for(s.centre_sequence, False)
print 'Blasting: %s...' % (seq[:60])
result_handle = NCBIWWW.qblast('blastn', db, seq)
blast_results = result_handle.read()
blast_out = cStringIO.StringIO(blast_results)
b_record = b_parser.parse(blast_out)
for alignment in b_record.alignments:
for hsp in alignment.hsps:
if hsp.expect < E_VALUE_THRESH:
print '****Alignment****'
print 'sequence:', alignment.title
print 'length:', alignment.length
print 'e value:', hsp.expect
print 'sbjct_start:', hsp.sbjct_start
print hsp.query[0:75] + '...'
print hsp.match[0:75] + '...'
print hsp.sbjct[0:75] + '...'
break
break
def blast(blastRootDirectory):
if sys.platform == 'win32':
blast_db = os.path.join(blastRootDirectory, 'blastDB.fasta')
else:
if not os.path.isdir('/tmp/BLAST'):
print "making directory '/tmp/BLAST'"
os.mkdir('/tmp/BLAST/')
if not os.path.exists('/tmp/BLAST/formatdb'):
shutil.copy(os.path.join(blastRootDirectory, 'formatdb'),
'/tmp/BLAST')
print "copying 'formatdb' to '/tmp/BLAST/'"
blast_db = os.path.join('/tmp/BLAST', 'blastDB.fasta')
#print 'path to blastDB.fasta:', blast_db
blast_file = os.path.join(blastRootDirectory, 'filetoblast.txt')
#print 'path to filetoblast.txt:', blast_file
if sys.platform == 'win32':
blastall_name = 'Blastall.exe'
blast_exe = os.path.join(blastRootDirectory, blastall_name)
else:
blastall_name = 'blastall'
blast_exe = os.path.join(os.getcwd(), '../../BLAST/bin/',
blastall_name)
#print 'path to blastall:', blast_exe
if sys.platform == 'win32':
import win32api
blast_db = win32api.GetShortPathName(blast_db)
blast_file = win32api.GetShortPathName(blast_file)
blast_exe = win32api.GetShortPathName(blast_exe)
#cont = raw_input('blah')
#try:
blast_out, error_info = NCBIStandalone.blastall(blast_exe,
'blastp',
blast_db,
blast_file,
align_view=7)
#except:
# f = open(blast_file, 'r')
# s = file.read()
# print s
#print 'done BLASTing'
print 'errors:', error_info.read()
print 'blast output:', blast_out.read()
b_parser = NCBIXML.BlastParser()
#print 'got parser'
b_record = b_parser.parse(blast_out)
b_iterator = NCBIStandalone.Iterator(blast_out, b_parser)
#print 'got iterator'
results = []
recordnumber = 0
nonmatchingQueries = []
while 1:
recordnumber += 1
b_record = b_iterator.next()
if not b_record: break
print 'query:', b_record.query
if b_record is None:
break
e_value_thresh = 0.001
print 'number of alignments:', len(b_record.alignments)
significant = False
for alignment in b_record.alignments:
for hsp in alignment.hsps:
if hsp.expect < e_value_thresh:
alignment.title = alignment.title.replace(">", "")
if b_record.query != alignment.title:
significant = True
print 'adding', b_record.query, 'and', alignment.title, 'to the list of matches'
results.append(
(b_record.query, alignment.title, hsp.expect))
print b_record.query, significant
if not significant:
print 'adding', b_record.query, 'to the list of queries without matches'
nonmatchingQueries.append(b_record.query)
return nonmatchingQueries, results
