def annotation_regulator(args):
if hasattr(args, 'temp_dir'):
args.annotation_dir = os.path.join(args.temp_dir, 'annotation')
else:
args.annotation_dir = os.path.join(os.getcwd(), 'annotation')
try:
safe_makedirs(args.annotation_dir)
except FileExistsError:
print('Diretory exist before validating, please check and remove it to prevent data loss.')
return False
except Exception:
print('Cannot make annotation temp folder!')
return False
valid = True
if args.max_contig_length < 0:
print('Please input valid contig length.')
valid = False
if args.hmmer_score < 0:
print('Please input valid hmmer score valve.')
valid = False
if args.hmmer_e < 0:
print('Please input valid hmmer e-value limit.')
valid = False
return valid
def search_regulator(args):
valid = True
if args.min_abundance <= 0:
print("Input minimum abundance is not valid.")
valid = False
from ete3 import NCBITaxa
ncbi = NCBITaxa()
if hasattr(args, 'temp_dir'):
args.findmitoscaf_dir = os.path.join(args.temp_dir, 'findmitoscaf')
else:
args.findmitoscaf_dir = os.path.join(os.getcwd(), 'findmitoscaf')
try:
safe_makedirs(args.findmitoscaf_dir)
except FileExistsError:
valid = False
print('Diretory exist before validating, please check and remove it to prevent data loss.')
except Exception:
valid = False
print('Error occured when validating the directories, please check your permissions or things could be related.')
if args.required_taxa not in ncbi.get_name_translator([args.required_taxa]):
print("Specified taxanomy name not in NCBI taxanomy database.")
return False
args.taxa_ids = ncbi.get_name_translator([args.required_taxa])[
args.required_taxa]
return valid
def assembly_regulator(args):
valid = True
if hasattr(args, 'temp_dir'):
args.assemble_dir = os.path.join(args.temp_dir, 'assemble')
else:
args.assemble_dir = os.path.join(os.getcwd(), 'assemble')
try:
safe_makedirs(args.assemble_dir)
except FileExistsError:
print('Diretory exist before validating, please check and remove it to prevent data loss.')
valid = False
except Exception:
valid = False
print('Error occured when validating the directories, please check your permissions or things could be related.')
args.kmer_list = [int(x) for x in args.kmer_list.split(',')]
args.kmer_list.sort()
if 0 in [x % 2 for x in args.kmer_list]:
print('All kmer length must be odd.')
valid = False
args.depth_list = [int(x) for x in args.depth_list.split(',')]
if args.prune_depth < 0:
print('Prune depth lower than 0.')
valid = False
return valid
def initialize(self):
self.basedir = path.abspath(self.basedir)
self.fq1 = path.abspath(self.fq1)
if self.fq2:
self.fq2 = path.abspath(self.fq2)
# Check if POPCNT command is supported
if self.use_popcnt:
if shell_call('megahit_core checkpopcnt').rstrip() != '1':
self.use_popcnt = False
logger.log(3, "POPCNT is disabled since no features detected.")
else:
self.hwaccel = shell_call(
"megahit_core checkcpu").rstrip() == '1'
logger.log(
2,
f"Using megahit with {'POPCNT' if not self.hwaccel else 'hardware acceleration'} support."
)
else:
logger.log(2, "POPCNT disabled by argument.")
if self.one_pass:
logger.log(3, "Using 1-pass mode.")
self.result_dir = safe_makedirs(
path.join(self.basedir, f'{self.prefix}.result'), False)
if not path.isdir(str(a_conf.external_temp)):
self.temp_dir = safe_makedirs(
path.join(self.basedir, f'{self.prefix}.temp'), False)
else:
self.temp_dir = safe_makedirs(
path.join(a_conf.external_temp, str(uuid.uuid4()),
f'{self.prefix}.temp'), False)
self.read_lib = path.join(self.temp_dir, 'reads.lib')
self.contig_dir = safe_makedirs(
path.join(self.temp_dir, 'intermediate_contigs'), False)
vm = psutil.virtual_memory()
logger.log(
1,
f"System memory status : {', '.join([f'{k}={v/(1024**2):.2f}MB' for k,v in vm._asdict().items() if type(v) is int])}"
)
self.available_memory = int(vm.available * a_conf.max_mem_percent)
logger.log(
2, f'Scheduled {self.available_memory/(1024**2):.2f}MB to use.')
def filter_regulator(args):
if hasattr(args, 'disable_filter') and args.disable_filter:
return True
valid = True
try:
args.start, args.end, *_ = [int(x) if int(x) > 0 else 0
for x in args.keep_region.split(',')]
except Exception:
print('Input range is not valid.')
valid = False
if hasattr(args, 'temp_dir'):
args.clean_dir = os.path.join(args.temp_dir, 'cleandata')
else:
args.clean_dir = os.path.join(os.getcwd(), 'cleandata')
try:
safe_makedirs(args.clean_dir)
except FileExistsError:
valid = False
print('Diretory exists before validating, please check and remove it to prevent data loss.')
except Exception:
valid = False
print('Error occured when validating the directories, please check your permissions or things could be related.')
if args.quality_valve <= 0 or args.quality_valve >= 255:
print('Input quality limit is not valid.')
valid = False
if args.Ns_valve <= 0:
print('Input N limit is not valid.')
valid = False
if args.percentage_valve <= 0 or args.percentage_valve >= 1:
print('Input percentage limit is not valid.')
valid = False
if args.trimming < 0:
print('Trimming value is not valid.')
valid = False
args.trimming = int(float(args.trimming) * (10**9))
return valid
def universal_regulator(args):
args.work_dir = os.path.abspath(os.path.join(args.basedir, args.workname))
args.result_dir = os.path.abspath(os.path.join(
args.work_dir, args.workname + '.result'))
args.temp_dir = os.path.abspath(os.path.join(
args.work_dir, args.workname + '.temp'))
# Validates the folders
try:
safe_makedirs(args.work_dir)
safe_makedirs(args.result_dir)
safe_makedirs(args.temp_dir)
except FileExistsError:
print('Diretory exist before validating, please check and remove it to prevent data loss.')
return False
except Exception:
print(
'Error occured when validating the directories, please check your permissions or things could be related.')
return False
tr = os.cpu_count()
tr = tr if tr is not None else 8
if args.threads <= 0 or args.threads > tr:
print(
f"Specified thread number not in range, using {tr} threads instead.")
args.threads = tr
args.level = ['code', 'debug', 'info',
'warn', 'error'].index(args.level)
if args.level == 0:
print("Using logger level 0, this could lead to a very verbose logging.")
return True
def _graph_prefix(self, kmer):
return path.join(
safe_makedirs(path.join(self.temp_dir, f'k{kmer}'), True),
str(kmer))