def getHits(gene):
''' BLAST parser using Biopython
Input: name of blast out file in standard ouput format
Outputs: 2 files
'''
inf = open(o.blast, 'rU')
parser = NCBIStandalone.BlastParser()
error_parser = NCBIStandalone.BlastErrorParser(inf)
iterator = NCBIStandalone.Iterator(inf, error_parser)
err_iterator = NCBIStandalone.Iterator(inf, error_parser)
#next_record =
## *** Parsing *** ##
lg = len(gene)
if o.verbose == True:
sys.stderr.write("\nGetting hits...\n")
for record in iterator:
query = record.query.split(" ")[0]
if query in gene:
out.write("%s\n" % gene[query])
if record.alignments is []:
out.write("%s\tNA\tNA\tNA\n" % gene[query])
else:
flag = 0
for alignment in record.alignments:
for hsp in alignment.hsps:
#-->## ** Selection Process **##
if float(hsp.expect) < 0.0001 and flag < 3:
out.write(
"%s\t%s\t%s\tHigh\n" %
(gene[query], alignment.title.split(">")[1],
float(hsp.expect)))
flag += 1
elif float(hsp.expect) < 1.0 and flag < 3:
out.write(
"%s\t%s\t%s\tLow\n" %
(gene[query], alignment.title.split(">")[1],
float(hsp.expect)))
flag += 1
elif float(hsp.expect) < 5.0 and flag < 3:
out.write(
"%s\t%s\t%s\tScare\n" %
(gene[query], alignment.title.split(">")[1],
float(hsp.expect)))
flag += 1
elif float(hsp.expect) > 1.0 and flag < 1:
out.write("%s\tNA\tNA\tNA\n" % gene[query])
flag += 1
del gene[query]
if o.verbose == True:
sys.stderr.write('\r' + '' * 0)
sys.stderr.write(str(int((lg - len(gene)) * 100 / lg)) + '%')
sys.stdout.flush()
else:
pass
if (lg - len(gene)) != len(gene):
sys.stderr.write("\nGenes not found:\n%s" % gene.keys())
def blast2data(filehandle): ###This should be for blast-txt
"""BLAST output to data dict"""
data = {}
blast_parser = NCBIStandalone.BlastParser()
blast_iterator = NCBIStandalone.Iterator(filehandle, blast_parser)
for blast_record in blast_iterator:
readname = blast_record.query.split()[0]
for alignment in blast_record.alignments:
if re.search("\|", alignment.title):
fields = alignment.title[1:].strip().split('|')
refgi = fields[1]
else:
fields = alignment.title[1:].strip().split(' ')
refgi = fields[0]
for hsp in alignment.hsps:
if hsp.expect > EVALUE_CUTOFF:
continue
identity = round(
float(hsp.identities[0]) * 100 / hsp.identities[1], 1)
start = hsp.sbjct_start
end = hsp.sbjct_end
if start > end:
tmp = start
start = end
end = tmp
if not data.has_key(refgi):
data[refgi] = []
if not refgi in references:
references.append(refgi)
refgenome2json(refgi)
if not refLengths.has_key(refgi):
refLengths[refgi] = gi2length(refgi)
data[refgi].append([start, identity, end, readname])
return data
def getCoordinatesFromBlo(bloFname, padding):
'''
# Extract coordinates from blo file
'''
coord = {}
#outf = open(outFile, 'w')
blast_parser = NCBIStandalone.BlastParser()
blast_iterator = NCBIStandalone.Iterator(open('temp.blo'), blast_parser)
#blast_iterator = SearchIO.parse(open('temp.blo'),'blast-txt') #if switch to SearchIO, this is the way to go (not working yet)
for hit in blast_iterator:
for alignment in hit.alignments:
for hsp in alignment.hsps:
#print alignment.title
#print hsp.sbjct_start, hsp.sbjct_end
#print hsp.sbjct
#outf.write("%s_%s-%s\n%s\n\n"%(alignment.title, hsp.sbjct_start, hsp.sbjct_end, hsp.sbjct))
new = True
fullName = alignment.title.replace('>', '')
if fullName in coord.keys() and hsp.sbjct_start >= coord[
fullName][0] and hsp.sbjct_end <= coord[fullName][1]:
new = False
if new:
coord[fullName] = [hsp.sbjct_start, hsp.sbjct_end]
return coord
def blast_parse(file, e, output):
result_handle = open(file)
blast_parser = NCBIStandalone.BlastParser()
blast_iterator = NCBIStandalone.Iterator(result_handle, blast_parser)
blast_record = next(blast_iterator)
output = open(output, 'w')
output.write('query title\tdescription\tlength\te value' + '\n')
for blast_record in blast_iterator:
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
if hsp.expect < e:
output.write(str(blast_record.query[:18]) + ' \t')
output.write(str(alignment.title) + '\t')
output.write(str(alignment.length) + '\t')
output.write(str(hsp.expect) + '')
output.write('\n')
output.close()
def __init__(self, handle):
"""Initialize the class."""
self.handle = handle
blast_parser = NCBIStandalone.BlastParser()
self.blast_iter = NCBIStandalone.Iterator(handle, blast_parser)
dbFile = argv[2]
outFile = argv[3]
#padding = int(argv[4])
# Format dbFile
if os.path.exists("%s.nin" % dbFile):
print "--[WARNING]blastdb already formated, using the existing one."
else:
print "Formatting database..."
os.system('formatdb -i %s -p F' % dbFile)
# Run BLAST
os.system(
'blastall -p blastn -i %s -d %s -e 1e-10 -v 100000 -b 100000 -m 0 -o temp.blo -q -2'
% (queryFile, dbFile))
# Extract sequeces from blo file
outf = open(outFile, 'w')
blast_parser = NCBIStandalone.BlastParser()
blast_iterator = NCBIStandalone.Iterator(open('temp.blo'), blast_parser)
#blast_iterator = SearchIO.parse(open('temp.blo'),'blast-txt') #if switch to SearchIO, this is the way to go (not working yet)
for hit in blast_iterator:
for alignment in hit.alignments:
for hsp in alignment.hsps:
#print alignment.title
#print hsp.sbjct_start, hsp.sbjct_end
#print hsp.sbjct
outf.write(
"%s_%s-%s\n%s\n\n" %
(alignment.title, hsp.sbjct_start, hsp.sbjct_end, hsp.sbjct))
# biopython
from Bio.Blast import NCBIStandalone
my_blast_db = os.path.join(os.getcwd(), 'at-est', 'a_cds-10-7.fasta')
my_blast_file = os.path.join(os.getcwd(), 'at-est', 'test_blast',
'sorghum_est-test.fasta')
my_blast_exe = os.path.join(os.getcwd(), 'blast', 'blastall')
print 'Running blastall...'
blast_out, error_info = NCBIStandalone.blastall(my_blast_exe, 'blastn',
my_blast_db, my_blast_file)
b_parser = NCBIStandalone.BlastParser()
b_iterator = NCBIStandalone.Iterator(blast_out, b_parser)
while 1:
b_record = b_iterator.next()
if b_record is None:
break
E_VALUE_THRESH = 0.04
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
def __init__(self, handle):
self.handle = handle
blast_parser = NCBIStandalone.BlastParser()
self.blast_iter = NCBIStandalone.Iterator(handle, blast_parser)
import string
from Bio.Seq import Seq
from Bio.Blast import NCBIStandalone
import fileinput
import glob
OutFile = r'Blast\out\02.blast_result_total.txt'
f = open(OutFile, 'r')
Mismatch_total_file = open('Mismatch_total_LOD v3_171103.txt', 'w')
blast_parser = NCBIStandalone.BlastParser()
print blast_parser
iterator = NCBIStandalone.Iterator(f, blast_parser)
for record in iterator:
for alignment in record.alignments:
for hsp in alignment.hsps:
mismatch_Number = (hsp.identities[1] -
(hsp.identities[0] + hsp.gaps[0]))
Gaps_Number = hsp.gaps[0]
if (mismatch_Number != 0):
Mismatch_total_file.write('%s\t%s\t%s\t%s\n' %
(record.query, alignment.title,
mismatch_Number, Gaps_Number))
f.close()
Mismatch_total_file.close()
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
argparser.add_argument('-d', '--dump', type=argparse.FileType('w'),
dest='dump_file',
help='pickle intermediate results in tempfile')
argparser.add_argument('-l', '--load', type=argparse.FileType('r'),
dest='load_file',
help='depickle intermediate results from tempfile')
argparser.add_argument('-o', '--outfile', type=argparse.FileType('w'), default=sys.stdout)
args = argparser.parse_args()
assert not (args.load_file and args.dump_file)
parser1 = NCBIStandalone.BlastParser()
parser2 = NCBIStandalone.BlastParser()
# PXL: PMZ(Q) x Lamp3(S), LXP: Lamp3(Q) x PMZ(S)
pxl_records = NCBIStandalone.Iterator(args.blast1, parser1)
lxp_records = NCBIStandalone.Iterator(args.blast2, parser2)
pxl_re = re.compile(r'(PMZ_[^\s]+)')
pxl_key_fn = lambda k: pxl_re.findall(k)[0]
lxp_re = re.compile(r'(lamp3[^\s]+ [^\s]+ len\d+)') # matching 'not whitespace' is faster and more robust
lxp_key_fn = lambda k: lxp_re.findall(k)[0]
pxl_lookup, lxp_lookup = None, None
if args.load_file:
pxl_lookup = cPickle.load(args.load_file)
lxp_lookup = cPickle.load(args.load_file)
else:
pxl_lookup = make_lookup(pxl_records, pxl_key_fn)
lxp_lookup = make_lookup(lxp_records, lxp_key_fn)
def ReadBlast(self, file, OUT, iszipped=0, is_psiblast=None):
output = open(OUT, "w")
self.selfhits = []
if is_psiblast:
print >> sys.stderr, 'Parsing PSI-Blast'
self.parser = NCBIStandalone.PSIBlastParser()
else:
self.parser = NCBIStandalone.BlastParser()
if file[-3:] == '.gz' or iszipped:
handle = gzip.open(file)
else:
handle = open(file)
self.iter = NCBIStandalone.Iterator(handle=handle, parser=self.parser)
self.blastDict = {}
while 1:
try:
rec = self.iter.next()
if not rec: break
except:
sys.stderr.write(
'Can\'t iterate on blast records anymore. Abort.\n')
import traceback
traceback.print_exc()
return 'Error parsing %s' % file
self.query = rec.query.split(" ")[
0] ## blast_record.query.split(" ")[0]
self.length = rec.query_letters
if self.length < self.min_size:
self.printer("Does not meet the minimum length " +
str(self.min_size))
break
if is_psiblast: rec = rec.rounds[-1]
# each alignment is one potential hit
for n, alignment in enumerate(rec.alignments):
hsp = alignment.hsps[0] #no multiple hsps
alnlength = hsp.align_length
hit = alignment.title
#targetlength = alignment.length
#m = re.search("sp\|([A-Z0-9]+)\|([A-Z0-9_]+) ?(.+)?", alignment.title)
m = re.search("sp\|(.+?)\|(.+?) (.+)?", alignment.title)
if m: # pyphynr blast result
hit_sp_ac = m.group(1)
hit_sp_id = m.group(2)
hit_sp_note = m.group(3)
elif alignment.title[
0] == '>': # result from qadditional blast databases
hit_sp_ac = None
hit_sp_id = alignment.title[1:].split()[0]
hit_sp_note = None
else:
hit_sp_ac = None
hit_sp_id = None
hit_sp_note = None
self.printer(hit_sp_id)
similarity = hsp.positives[0] / float(hsp.positives[1]) * 100
if float(hsp.expect) <= float(self.HSP_max_evalue):
if float(similarity) >= int(self.HSP_minimal_positives):
coverage = hsp.positives[1] / float(self.length) * 100
if float(coverage) >= int(self.HSP_minimal_coverage):
#targetcoverage = hsp.positives[1]/float(targetlength)*100
#if float(targetcoverage) > int(self.HSP_minimal_targetcov):
#self.compatibles.append((hit_sp_ac, hit))
#hitlist = [hit_sp_id, n+1 , hsp.positives[0]/float(hsp.positives[1])*100, hsp.positives[1]/float(self.length)*100, hsp.positives[1]/float(targetlength)*100, hsp.score, hsp.expect]
hitlist = [
hit_sp_id, hsp.positives[0] /
float(hsp.positives[1]) * 100,
hsp.positives[1] / float(self.length) * 100,
hsp.score, hsp.expect
]
if self.cB: self.createblastDict(query, hitlist)
output.write("%s\t" % (self.query)),
for element in hitlist:
output.write("%s\t" % element),
output.write("\n")
output.close()
handle.close()
return None
aster = []
for t, pair in enumerate(zip(query, sbjct), 1):
q, s = pair
if q == 'N':
aster.append([t, q, s])
return aster
if __name__ == "__main__":
blast_parser = NCBIStandalone.BlastParser()
GLB = glob.glob('*.nofmt')
for glb in GLB:
handle = open(glb, 'r')
blast_iterator = NCBIStandalone.Iterator(handle, blast_parser)
total = 0
E_VALUE_THRESH = 1
with open(glb[:-6] + ".csv", 'w') as outcsv:
for blast_record in blast_iterator:
print("query:", blast_record.query)
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
if hsp.expect < E_VALUE_THRESH:
if hsp.align_length < 100:
continue
if len(str(hsp.sbjct)) == 0:
continue
print(hsp.query)
print(hsp.match)
print(hsp.sbjct)
