def __init__(self, args):
"""Run all checks needed to create a FastQMCFTrimPairs object
Check that fastq-mcf exists in the system
Specify the fasta adapter file and any arguments
Create the output folder
:param args: an object with settable and gettable attributes
:type args: Namespace, SimpleNamespace, etc.
"""
argfiller = ArgFiller(args)
argfiller.fill(['root', 'adapters', 'fastq', 'fastq_args', 'quiet'])
self.root = args.root
self.adapters = args.adapters
self.fastq_args = args.fastq_args
self.executable = args.fastq
self.quiet = args.quiet
self.outdir = os.path.join(self.root, 'trimmed')
try:
os.makedirs(self.outdir)
except OSError:
if not os.path.isdir(self.outdir):
raise
try:
with open(os.devnull, "w") as fnull:
subprocess.call([self.executable], stdout=fnull, stderr=fnull)
except OSError:
self.logger.error(
'fastq-mcf not found, cannot use FastQMCFTrimPairs')
raise
else:
self.logger.info('fastq-mcf found')
def __init__(self, args):
"""Run all checks needed to create a FastQMCFTrimPairs object
Check that fastq-mcf exists in the system
Specify the fasta adapter file and any arguments
Create the output folder
:param args: an object with settable and gettable attributes
:type args: Namespace, SimpleNamespace, etc.
"""
argfiller = ArgFiller(args)
argfiller.fill(["root", "adapters", "fastq", "fastq_args", "quiet"])
self.root = args.root
self.adapters = args.adapters
self.fastq_args = args.fastq_args
self.executable = args.fastq
self.quiet = args.quiet
self.outdir = os.path.join(self.root, "trimmed")
try:
os.makedirs(self.outdir)
except OSError:
if not os.path.isdir(self.outdir):
raise
try:
with open(os.devnull, "w") as fnull:
subprocess.call([self.executable], stdout=fnull, stderr=fnull)
except OSError:
self.logger.error("fastq-mcf not found, cannot use FastQMCFTrimPairs")
raise
else:
self.logger.info("fastq-mcf found")
def __init__(self, args):
"""Prepare the recursive file finder
Check that a root directory is provided, or ask for one
Make sure the search extension is valid
:param args: an object with settable and gettable attributes
:type args: Namespace, SimpleNamespace, etc.
"""
argfiller = ArgFiller(args)
argfiller.fill(['root', 'ext'])
self.root = args.root
self.ext = args.ext
def __init__(self, args):
"""Prepare the recursive file finder
Check that a root directory is provided, or ask for one
Make sure the search extension is valid
:param args: an object with settable and gettable attributes
:type args: Namespace, SimpleNamespace, etc.
"""
argfiller = ArgFiller(args)
argfiller.fill(["root", "ext"])
self.root = args.root
self.ext = args.ext
def __init__(self, args):
"""Prepare for the merge file stage
Check for a root directory and a blocksize
:param args: an object with settable and gettable attributes
:type args: Namespace, SimpleNamespace, etc.
"""
argfiller = ArgFiller(args)
argfiller.fill(["root", "ext", "blocksize"])
self.root = args.root
self.blocksize = args.blocksize
self.ext = args.ext
self.outdir = os.path.join(self.root, "merged")
try:
os.makedirs(self.outdir)
except OSError:
if not os.path.isdir(self.outdir):
self.logger.error("Cannot make directory {0}, " "permissions".format(self.outdir))
raise
def __init__(self, args):
"""Prepare for the merge file stage
Check for a root directory and a blocksize
:param args: an object with settable and gettable attributes
:type args: Namespace, SimpleNamespace, etc.
"""
argfiller = ArgFiller(args)
argfiller.fill(['root', 'ext', 'blocksize'])
self.root = args.root
self.blocksize = args.blocksize
self.ext = args.ext
self.outdir = os.path.join(self.root, 'merged')
try:
os.makedirs(self.outdir)
except OSError:
if not os.path.isdir(self.outdir):
self.logger.error('Cannot make directory {0}, '
'permissions'.format(self.outdir))
raise