def _netblast_search(self, fastaRecord, excludelist=[], usecache=True):
"""
Blast against genbank over web
"""
### THIS IS A HACK FOR TESTING PURPOSES TO REMOVED AGAIN ##########################################
if self.options.ONEMISSING:
orig_limit_query = self.options.limitquery
genus, species = re.search(r'_([^_]+)_([^_]+)$',
fastaRecord.title).groups()
self.options.limitquery = "barcode[keyword] NOT %s %s[ORGN]" % (
genus, species)
print "REFORMATTING LIMIT QUERY TO", self.options.limitquery
### THIS IS A HACK FOR TESTING PURPOSES TO REMOVED AGAIN ##########################################
# Make a query to filter the returned results:
if excludelist:
entrezQuery = '(' + self.options.limitquery + ') NOT (uncultured[WORD] OR ' + '[ORGN] OR '.join(
excludelist) + '[ORGN])'
else:
entrezQuery = '(' + self.options.limitquery + ') NOT uncultured[WORD]'
### THIS IS A HACK FOR TESTING PURPOSES TO REMOVED AGAIN ##########################################
if self.options.ONEMISSING:
self.options.limitquery = orig_limit_query
### THIS IS A HACK FOR TESTING PURPOSES TO REMOVED AGAIN ##########################################
fileSuffix = ''
for name in excludelist:
l = re.split(r'\s+', name)
for n in l:
fileSuffix += n[0]
if fileSuffix:
fileSuffix = '_' + fileSuffix
# File name used for blast cache
blastFileName = os.path.join(
self.options.blastcache,
"%s.%d_%s%s.xml" % (fastaRecord.title, self.options.maxblasthits,
self.options.minsignificance, fileSuffix))
if usecache and os.path.exists(
blastFileName) and os.path.getsize(blastFileName) > 0:
# Use cached blast result
if excludelist:
print "\n\t\tUsing cached Blast results (excluding %s)..." % ', '.join(
excludelist),
else:
print "\n\t\tUsing cached Blast results...",
sys.stdout.flush()
else:
# Make a query to filter the returned results:
if excludelist:
print "\n\t\tSearching database (excluding %s)..." % ', '.join(
excludelist),
else:
print "\n\t\tSearching database...",
sys.stdout.flush()
fastaRecordFileName = os.path.join(self.options.project,
utils.randomString(8))
fastaRecordFile = open(fastaRecordFileName, 'w')
fastaRecordFile.write(str(fastaRecord))
fastaRecordFile.close()
resultHandle = None
if self.options.nolowcomplexfilter:
filterOption = '-dust no'
else:
filterOption = '-dust yes' # FIXME: Check that this is an ok default... It is not the defalut in blastn
if self.options.blastwordsize:
wordSize = '-word_size %s' % self.options.blastwordsize
else:
wordSize = ''
blastCmd = 'blastn -remote -outfmt 5 -db nt %s %s -evalue %s -max_target_seqs %s -entrez_query "%s" -query %s -out %s' \
% (wordSize, filterOption, self.options.minsignificance, self.options.maxblasthits, \
entrezQuery, fastaRecordFileName, blastFileName)
for i in range(20):
time.sleep(2 * i)
error = utils.systemCall(blastCmd,
stdout='IGNORE',
stderr='IGNORE')
try:
# retval = os.system(blastCmd)
# if retval != 0:
# print "Netblast failed with return value %d. Trying again..." % retval
error = utils.systemCall(blastCmd)
if error or not os.path.exists(
blastFileName) or os.path.getsize(
blastFileName) == 0:
print "Netblast failed. Trying again..."
continue
break
except KeyboardInterrupt:
sys.exit()
except:
print "Netblast failed. Trying again..."
pass
os.remove(fastaRecordFileName)
# Read file from cache
blastHandle = open(blastFileName, 'r')
# Parse the result:
try:
blastRecord = NCBIXML.read(blastHandle)
print "done.\n\t\t\t",
sys.stdout.flush()
except:
blastRecord = None
blastHandle.close()
return blastRecord
def _netblast_search(self, fastaRecord, excludelist=[], usecache=True):
"""
Blast against genbank over web
"""
### THIS IS A HACK FOR TESTING PURPOSES TO REMOVED AGAIN ##########################################
if self.options.ONEMISSING:
orig_limit_query = self.options.limitquery
genus, species = re.search(r'_([^_]+)_([^_]+)$', fastaRecord.title).groups()
self.options.limitquery = "barcode[keyword] NOT %s %s[ORGN]" % (genus, species)
print "REFORMATTING LIMIT QUERY TO", self.options.limitquery
### THIS IS A HACK FOR TESTING PURPOSES TO REMOVED AGAIN ##########################################
# Make a query to filter the returned results:
if excludelist:
entrezQuery = '(' + self.options.limitquery + ') NOT (uncultured[WORD] OR ' + '[ORGN] OR '.join(excludelist) + '[ORGN])'
else:
entrezQuery = '(' + self.options.limitquery + ') NOT uncultured[WORD]'
### THIS IS A HACK FOR TESTING PURPOSES TO REMOVED AGAIN ##########################################
if self.options.ONEMISSING:
self.options.limitquery = orig_limit_query
### THIS IS A HACK FOR TESTING PURPOSES TO REMOVED AGAIN ##########################################
fileSuffix = ''
for name in excludelist:
l = re.split(r'\s+', name)
for n in l:
fileSuffix += n[0]
if fileSuffix:
fileSuffix = '_' + fileSuffix
# File name used for blast cache
blastFileName = os.path.join(self.options.blastcache, "%s.%d_%s%s.xml" % (fastaRecord.title,
self.options.maxblasthits, self.options.minsignificance, fileSuffix))
if usecache and os.path.exists(blastFileName) and os.path.getsize(blastFileName)>0:
# Use cached blast result
if excludelist:
print "\n\t\tUsing cached Blast results (excluding %s)..." % ', '.join(excludelist),
else:
print "\n\t\tUsing cached Blast results...",
sys.stdout.flush()
else:
# Make a query to filter the returned results:
if excludelist:
print "\n\t\tSearching database (excluding %s)..." % ', '.join(excludelist),
else:
print "\n\t\tSearching database...",
sys.stdout.flush()
fastaRecordFileName = os.path.join(self.options.project, utils.randomString(8))
fastaRecordFile = open(fastaRecordFileName, 'w')
fastaRecordFile.write(str(fastaRecord))
fastaRecordFile.close()
resultHandle = None
if self.options.nolowcomplexfilter:
filterOption = '-dust no'
else:
filterOption = '-dust yes' # FIXME: Check that this is an ok default... It is not the defalut in blastn
if self.options.blastwordsize:
wordSize = '-word_size %s' % self.options.blastwordsize
else:
wordSize = ''
blastCmd = 'blastn -remote -outfmt 5 -db nt %s %s -evalue %s -max_target_seqs %s -entrez_query "%s" -query %s -out %s' \
% (wordSize, filterOption, self.options.minsignificance, self.options.maxblasthits, \
entrezQuery, fastaRecordFileName, blastFileName)
for i in range(20):
time.sleep(2 * i)
error = utils.systemCall(blastCmd, stdout='IGNORE', stderr='IGNORE')
try:
# retval = os.system(blastCmd)
# if retval != 0:
# print "Netblast failed with return value %d. Trying again..." % retval
error = utils.systemCall(blastCmd)
if error or not os.path.exists(blastFileName) or os.path.getsize(blastFileName) == 0:
print "Netblast failed. Trying again..."
continue
break
except KeyboardInterrupt:
sys.exit()
except:
print "Netblast failed. Trying again..."
pass
os.remove(fastaRecordFileName)
# Read file from cache
blastHandle = open(blastFileName, 'r')
# Parse the result:
try:
blastRecord = NCBIXML.read(blastHandle)
print "done.\n\t\t\t",
sys.stdout.flush()
except:
blastRecord = None
blastHandle.close()
return blastRecord
