def __init__(self,
run_name,
platform,
unaligned_dir='bcl2fastq',
fmt='bcl2fastq2',
paired_end=True,
no_lane_splitting=False,
no_undetermined=False,
top_dir=None,
metadata=None,
readme=None):
# Make a mock-up of an analysis dir
self.run_name = os.path.basename(str(run_name))
self.platform = str(platform).lower()
self.readme = readme
# Store metadata
self.metadata = { 'run_name': self.run_name,
'platform': self.platform, }
if metadata is not None:
for item in metadata:
self.metadata[item] = metadata[item]
name = "%s_analysis" % run_name
if top_dir is None:
top_dir = os.getcwd()
MockIlluminaData.__init__(self,name,fmt,
unaligned_dir=unaligned_dir,
paired_end=paired_end,
no_lane_splitting=no_lane_splitting,
top_dir=top_dir)
# Add undetermined
if not no_undetermined:
self.add_undetermined()
def __init__(self,
run_name,
platform,
unaligned_dir='bcl2fastq',
fmt='bcl2fastq2',
paired_end=True,
lanes=None,
no_lane_splitting=False,
no_undetermined=False,
top_dir=None,
metadata=None,
readme=None):
# Make a mock-up of an analysis dir
self.run_name = os.path.basename(str(run_name))
self.platform = str(platform).lower()
self.readme = readme
# Store metadata
self.metadata = {
'run_name': self.run_name,
'platform': self.platform,
}
if metadata is not None:
for item in metadata:
self.metadata[item] = metadata[item]
name = "%s_analysis" % run_name
if top_dir is None:
top_dir = os.getcwd()
MockIlluminaData.__init__(self,
name,
fmt,
unaligned_dir=unaligned_dir,
paired_end=paired_end,
no_lane_splitting=no_lane_splitting,
top_dir=top_dir)
# Add undetermined
if not no_undetermined:
self.add_undetermined(lanes=lanes)
def __init__(self,
run_name,
platform,
unaligned_dir='bcl2fastq',
fmt='bcl2fastq2',
paired_end=True,
lanes=None,
no_lane_splitting=False,
no_undetermined=False,
top_dir=None,
metadata=None,
readme=None,
project_metadata=None):
"""
Create a mock-up of an analysis directory
Arguments:
run_name (str): name for the run e.g.
'1130904_PJB_XXXXX'
platform (str): name for the platform
e.g. 'nextseq'
unaligned_dir (str): for the bcl2fastq
output directory (default: 'bcl2fastq')
fmt (str): format of the outputs (can be
'casava' or 'bcl2fastq2'; default is
'bcl2fastq')
paired_end (bool): whether run should be
paired end (set True, default) or single
end (set False)
lanes (list): if not None then specify a
list of lane numbers to include
no_lane_splitting (bool): whether to
mimic the '--no-lane-splitting' option
of bcl2fastq2 in generating Fastq names
(default: make separate Fastqs for each
lane)
no_undetermined (bool): whether to
include 'undetermined' outputs (default:
False, do include 'undetermined'
outputs)
top_dir (str): set parent directory to
make the mock analysis directory in
(default: current working directory)
metadata (dict): if set then should be
a dictionary of metadata items with
corresponding values, which will be
written to the metadata.info file
readme (str): if set then will be
written to a 'README' file in the mock
analysis directory
project_metadata (dict): if set then should
be a dictionary where keys are names of
projects and values are dictionaries of
metadata items, which will be written to
the README.info file for that project
"""
# Make a mock-up of an analysis dir
self.run_name = os.path.basename(str(run_name))
self.platform = str(platform).lower()
self.readme = readme
# Store metadata
self.metadata = {
'run_name': self.run_name,
'platform': self.platform,
}
if metadata is not None:
for item in metadata:
self.metadata[item] = metadata[item]
self.project_metadata = dict()
if project_metadata is not None:
for project in project_metadata:
self.project_metadata[project] = \
project_metadata[project]
name = "%s_analysis" % run_name
if top_dir is None:
top_dir = os.getcwd()
MockIlluminaData.__init__(self,
name,
fmt,
unaligned_dir=unaligned_dir,
paired_end=paired_end,
no_lane_splitting=no_lane_splitting,
top_dir=top_dir)
# Add undetermined
if not no_undetermined:
self.add_undetermined(lanes=lanes)
