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())
