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 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)
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()
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,
