def gene_count(directory, summary_folder, chromosomes_folder, input_folder,
chromosomes_list, sam_file_list):
num_cores = Parallel.cpu_count()
print ">>> Using %d Processor Cores" % (num_cores - 1)
Parallel.Parallel(n_jobs=num_cores - 1)(Parallel.delayed(
lets_count)(directory, summary_folder, chromosomes_folder,
input_folder, chromosomes_list, f) for f in sam_file_list)
def gene_count(directory, summary_folder, chromosomes_folder, input_folder, chromosomes_list, sam_file_list):
num_cores = Parallel.cpu_count()
print ">>> Using %d Processor Cores" % (num_cores - 1)
_spin = spinbar.SpinCursor(msg="Processing mapped .sam files ...", speed=2)
_spin.start()
Parallel.Parallel(n_jobs=num_cores-1)(Parallel.delayed(letsCount)(directory, summary_folder, chromosomes_folder,
input_folder, chromosomes_list, f) for f in
sam_file_list)
_spin.stop()
def blast_search(self, directory, db_name, blast_results_folder,
blast_results_query):
platform_specific_path = 'osx'
suffix = ''
if _platform == "linux" or _platform == "linux2":
platform_specific_path = 'linux'
elif _platform == "darwin":
platform_specific_path = 'osx'
elif _platform.startswith('win'):
platform_specific_path = 'windows'
suffix = '.exe'
bit_size = 'x' + str(struct.calcsize("P") * 8)
blast_path = os.path.join(os.curdir, 'ncbi_blast', 'bin',
platform_specific_path, bit_size)
# self.fileio.check_path(os.curdir, blast_path, 'Cannot find relevant Blast programs in Resources folder')
blast_db = os.path.join(os.curdir, 'ncbi_blast', 'db')
# database_list = self.fileio.get_file_list(blast_db, ".fa")
# selection = select.Selection_Dialog()
# selection.windowTitle('Blast Database Selection')
# selection.populate_list(database_list)
# selection.exec_()
# selection.activateWindow()
# db_selection = selection.selection
db_path = os.path.join(blast_db, db_name)
print ">>> Selected Blast DB: %s" % db_name
sys.stdout.flush()
file_list = self.fileio.get_file_list(directory, blast_results_folder,
".fa")
for file_name in file_list:
output_file = os.path.join(
directory, blast_results_folder,
file_name.replace(".junctions.fa", '.blast.txt'))
print ">>> Running BLAST search for file: " + file_name
blast_command_list = [
os.path.join(blast_path, 'blastn' + suffix), '-query',
os.path.join(directory, 'blast_results', file_name), '-db',
db_path, '-task', 'blastn', '-dust', 'no', '-num_threads',
str(Parallel.cpu_count()), '-outfmt', '7', '-out', output_file,
'-evalue', '0.2', '-max_target_seqs', '10'
]
# blast_command = " ".join(blast_command_list)
sys.stdout.flush()
# os.system(blast_command)
self.blast_pipe = subprocess.Popen(blast_command_list, shell=False)
self.blast_pipe.wait()
def blast_search(self, directory, db_name, blast_results_folder):
platform_specific_path = 'osx'
suffix = ''
if _platform == "linux" or _platform == "linux2":
platform_specific_path = 'linux'
elif _platform == "darwin":
platform_specific_path = 'osx'
elif _platform.startswith('win'):
platform_specific_path = 'windows'
suffix = '.exe'
bit_size = 'x' + str(struct.calcsize("P") * 8)
blast_path = os.path.join(os.curdir, 'ncbi_blast', 'bin', platform_specific_path, bit_size)
# self.fileio.check_path(os.curdir, blast_path, 'Cannot find relevant Blast programs in Resources folder')
blast_db = os.path.join(os.curdir, 'ncbi_blast', 'db')
# database_list = self.fileio.get_file_list(blast_db, ".fa")
# selection = select.Selection_Dialog()
# selection.windowTitle('Blast Database Selection')
# selection.populate_list(database_list)
# selection.exec_()
# selection.activateWindow()
# db_selection = selection.selection
db_path = os.path.join(blast_db, db_name)
print ">>> Selected Blast DB: %s" % db_name
sys.stdout.flush()
for file_name in self.fileio.get_file_list(directory, blast_results_folder, ".fa"):
output_file = os.path.join(directory, blast_results_folder, file_name + '.blast.txt')
blast_command_list = [os.path.join(blast_path, 'blastn' + suffix),
'-query', os.path.join(directory, 'blast_results', file_name), '-db', db_path,
'-task', 'blastn', '-dust', 'no', '-num_threads', str(Parallel.cpu_count()),
'-outfmt', '7', '-out', output_file, '-evalue', '0.2', '-max_target_seqs', '10']
# blast_command = " ".join(blast_command_list)
print ">>> Running BLAST search for file: " + file_name
sys.stdout.flush()
self._spin = spinbar.SpinCursor(msg="Please wait for BLAST to finish...", speed=2)
self._spin.start()
# os.system(blast_command)
self.blast_pipe = subprocess.Popen(blast_command_list, shell=False)
self.blast_pipe.wait()
self._spin.stop()
