def process_contig(self):
"""Process nuclotide sequence(s)."""
file_name = os.path.basename(self.input_sequence)
output = self.output_file
tax_class = self.tax_class
print("OKOKOKOKOKOK")
orf_obj = ORF(input_file=self.input_sequence)
orf_obj.contig_to_orf()
contig_fsa_file = os.path.join(self.working_directory,
"{}.temp.contig.fsa".format(file_name))
try:
if os.stat(contig_fsa_file).st_size > 0:
if self.aligner == "diamond":
diamond_obj = Diamond(input_file=contig_fsa_file,
output_file=output,
tax_class=tax_class,
num_threads=self.threads)
diamond_obj.run()
else:
print(contig_fsa_file)
blast_obj = Blast(input_file=contig_fsa_file,
output_file=output,
tax_class=tax_class,
num_threads=self.threads)
blast_obj.run()
else:
self.write_stub_output_file()
except Exception as e:
pass
else:
pass
def test_interpertBlast(self):
tempBlast = Blast("", "")
tempBlast.makeDatabase("test_data/reference.fasta")
tempBlast.aliasTool("test_data/reference.fasta", "test_data")
tempBlast.query = "test_data/contigs_1.fasta"
tempBlast.doBlast("test_data")
tempBlast.interpertBlast("test_data")
self.assertEqual(len(tempBlast.hitSet), 3)
def __init__(self, args):
self.execution = 1
self.check_args(args)
bcontigfile = os.getcwd() + '/' + str(
args['sample']) + '/' + args['bcontigs']
if not os.path.exists(bcontigfile):
self.csv_to_fasta()
self.cmd = []
self.ssh_cmd = []
if self.execution == 1:
Blast.create_cmd(self)
def test_makeDatabase(self):
tempBlast = Blast("", "")
tempBlast.makeDatabase("test_data/reference.fasta")
workline = "blastdbcmd -db test_data/reference.fasta -info"
p = subprocess.Popen(workline, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
try:
stdout, stderr = p.communicate()
testResult = True
if p.returncode == 0:
if "1 sequences; 10,000 total bases" not in stdout:
testResult = False
self.assertTrue(testResult)
else:
raise EnvironmentError(stderr)
except EnvironmentError as error:
self.fail(error)
def process_protein(self):
"""Process protein sequence(s)."""
file_name = os.path.basename(self.input_sequence)
output = self.output_file
tax_class = self.tax_class
if self.aligner == "diamond":
diamond_obj = Diamond(self.input_sequence,
output_file=output,
tax_class=tax_class,
num_threads=self.threads)
diamond_obj.run()
else:
blast_obj = Blast(input_file=file_name,
output_file=output,
tax_class=tax_class,
num_threads=self.threads)
blast_obj.run()
def test_doBlast(self):
tempBlast = Blast("", "")
tempBlast.makeDatabase("test_data/reference.fasta")
tempBlast.aliasTool("test_data/reference.fasta", "test_data")
tempBlast.query = "test_data/contigs_1.fasta"
tempBlast.doBlast("test_data")
try:
outputFile = open("test_data/blastResult.csv")
testResult = True
for line in outputFile:
if "gi|49175990|ref|NC_000913.2|" not in line:
testResult = False
self.assertTrue(testResult)
except IOError as error:
self.fail(error)
def main():
# Define an argument parser to pull arguments from the command line
parser = argparse.ArgumentParser(
description='Run a local blast query on a variety of sequences.')
# f1 argument
parser.add_argument('-f',
metavar='-f',
nargs='+',
required=True,
help='A list of filenames or Refseq ids ')
# f2 argument
parser.add_argument('-g',
metavar='-g',
nargs='+',
required=True,
type=int,
help='Genomes passed by taxid: 9606, 562, 2697049')
# Output file
parser.add_argument('-o',
metavar='-o',
nargs='+',
required=True,
help='The name of the output file')
# e value argument
parser.add_argument('-e',
nargs='?',
default=10,
type=int,
help='e-value threshold. Defaults to 10.')
# Parse arguments
args = parser.parse_args()
# Generate the blast object with the arguments
blast = Blast(args)
# Get the filenames of the query sequences needed
filenames = blast.pull_sequences()
# Run the blast query
blast.format_file()
blast.run_blast(filenames)
FP1.close
expressions = []
FP2.readline()
for line in FP2:
temp = line.strip().split()
trID = temp[0]
dShift = temp[1]
hShock = temp[2]
loggrowth = temp[3]
pphase = temp[4]
dxp = DiffExp(trID, dShift, hShock, loggrowth, pphase)
expressions.append(dxp)
FP2.close
objblast = Blast(blast)
objmatrix = Matrix(expressions)
'''
Load the BlastHit objects that are good matches into a dictionary
'''
goodblasthits = {}
for item in objblast:
if item.good_match():
goodblasthits[item.TranscriptID] = item.SwissProtID
'''
create an output file
'''
FP3 = open("Output.txt", 'w')
FP3.write('{}\t{}\t{}\t{}\t{}\n'.format('','Sp_ds','Sp_hs', 'Sp_log', 'Sp_plat'))
player1 = players.sprites()[0]
player1.money = pm
moneycounter = CounterDisplay(player1.money,
(20, height - 10))
healthbar = HealthBar(player1, (50, 50))
if event.key == pygame.K_d or event.key == pygame.K_RIGHT:
player1.direction("right")
if event.key == pygame.K_a or event.key == pygame.K_LEFT:
player1.direction("left")
if event.key == pygame.K_w or event.key == pygame.K_UP:
player1.jump()
if event.key == pygame.K_s or event.key == pygame.K_DOWN:
player1.direction("down")
if event.key == pygame.K_SPACE:
Blast(player1.headingx, player1.rect.center)
if event.type == pygame.KEYUP:
if event.key == pygame.K_d or event.key == pygame.K_RIGHT:
player1.direction("stop right")
if event.key == pygame.K_a or event.key == pygame.K_LEFT:
player1.direction("stop left")
if event.key == pygame.K_w or event.key == pygame.K_UP:
player1.stop_jump()
if event.key == pygame.K_s or event.key == pygame.K_DOWN:
player1.direction("stop down")
playersHitBlocks = pygame.sprite.groupcollide(players, hardBlocks,
False, False)
enemiesHitBlocks = pygame.sprite.groupcollide(enemies, hardBlocks,
False, False)
enemiesHitEnemies = pygame.sprite.groupcollide(enemies, enemies, False,
"/MapperUnique.gff"))
methodList.append(PrimerDesign.PrimerDesign.runMethodSubstract([methodList[1], methodList[2]], Main.Main.workDir +
"/DenovoUnique.gff"))
genome = PrimerDesign.PrimerDesign.readRefGenome(Main.Main.genomeAdd + Main.Main.refGenomeList[0])
blastList = list()
for PipMethod in methodList:
fastaFile = PipMethod.rstrip()[:-3]+"fa"
PrimerDesign.PrimerDesign.saveFasta(fastaFile, PrimerDesign.PrimerDesign.readGFF(PipMethod, genome))
blastList.append(fastaFile)
otherGenomes = copy.copy(Main.Main.refGenomeList)
del otherGenomes[0]
blastThread = list()
allAlias = ""
for genome in otherGenomes:
Blast.makeDatabase(str(genome), Main.Main.workDir)
allAlias += Main.Main.workDir + "/" + genome + " "
allAlias = allAlias.rstrip()
Blast.aliasTool(allAlias, Main.Main.workDir)
for blastItem in blastList:
blastResult = Blast(blastItem, otherGenomes)
blastResult.start()
blastThread.append(blastResult)
for blastItem in blastThread:
blastItem.join()
genome = PrimerDesign.PrimerDesign.readRefGenome(Main.Main.genomeAdd + Main.Main.refGenomeList[0])
for k, blastItem in enumerate(blastList):
item = blastItem.rstrip()[:-2]
thread = threading.Thread(PrimerDesign.PrimerDesign.generatePrimer3Input(
def create_genouest_script(self):
Blast.create_genouest_script(self)
