def testRunBlastX(self):
"""
test running blastx
"""
## run the blast
self.blast = Blast(self.queryFile)
outFile = "adh-0-2.xml"
targetDB = os.path.join(self.BLASTDB, "uniprot_sprot")
start, stop = 0, 2
self.blast.run_blast(targetDB,
evalue=0.1,
start=start,
stop=stop,
cmd='blastx')
## read the blast
parser = ParseBlast(outFile)
parser.run()
## clean up
for fn in [
"adh-0-2_parsed.csv", "adh-0-2_parsed.log", "adh-0-2.fasta",
"adh-0-2.xml"
]:
self.assertTrue(os.path.exists(fn))
os.remove(fn)
def parse_file(self,resultsFilePath):
"""
use ParseBlast to parse a given xml formatted file
"""
print '...parsing', resultsFilePath
parser = ParseBlast(resultsFilePath,fhLog=self.logWriter,fhResults=self.resultsWriter)
parser.run()
## read input
if len(sys.argv) < 2:
raise Exception("\n\nInvalid syntax. use '%s'" % sys.argv[0] +
" -s source\n")
try:
optlist, args = getopt.getopt(sys.argv[1:], 's:')
except getopt.GetoptError:
raise Exception("\n\nInvalid syntax. use '%s'" % sys.argv[0] +
" -s source\n")
source = 'None'
for o, a in optlist:
if o == '-s':
source = a
if source not in ['dn', 'gg', 'reference']:
raise Exception("bad source specified")
outfmt = '5'
blastFile = "blast-%s.%s" % (source, "outfmt" + outfmt)
outFile = "blast-%s-parsed.csv" % source
if not os.path.exists(blastFile):
raise Exception("cannot find blast output file: %s" % blastFile)
## parse the resultsread the blast
parser = ParseBlast(blastFile, outFile=outFile)
parser.run()