def __init__(self, json_path, out_dir):
# Attributes #
self.out_dir = out_dir
self.json_path = FilePath(json_path)
# Parse #
self.info = load_json_path(self.json_path)
# Basic #
self.account = "/dev/null"
self.run_num = self.info['run_num']
self.run_label = "pyrosample_run_%i" % self.run_num
self.project_short_name = self.info['project']
self.project_long_name = self.info['project_name']
# Own attributes #
self.num = self.info['sample_num']
self.short_name = self.info['sample']
self.long_name = self.info['sample_name']
self.name = 'run%i_sample%i' % (self.run_num, self.num)
self.group = self.info['group']
self.id_name = "run%03d-sample%02d" % (self.run_num, self.num)
# Hard coded attributes #
self.machine = "454 GS FLX Titanium"
# SFF files #
self.sff_files_info = self.info['files']
# Pool dummy #
self.pool, self.parent = self, self
# Other dummy variables #
self.bar_len = 0
self.gzipped = False
self.used = True
# Loaded #
self.loaded = False
def __init__(self, json_path, out_dir):
# Attributes #
self.out_dir = out_dir
self.json_path = FilePath(json_path)
# Parse #
self.info = load_json_path(self.json_path)
# Basic #
self.account = self.info['uppmax_id']
self.run_num = self.info['run_num']
self.run_label = self.info['run_id']
self.project_short_name = self.info['project']
self.project_long_name = self.info['project_name']
self.fwd_name = self.info['forward_reads']
self.rev_name = self.info['reverse_reads']
# Own attributes #
self.num = self.info['sample_num']
self.label = self.info['sample_id']
self.short_name = self.info['sample']
self.long_name = self.info['sample_name']
self.name = 'run%i_sample%i' % (self.run_num, self.num)
self.group = self.info.get('group')
self.id_name = "run%03d-sample%02d" % (self.run_num, self.num)
self.fwd_mid = self.info['forward_mid']
self.rev_mid = self.info['reverse_mid']
self.used = True
# Check name is ASCII #
assert all(ord(c) < 128 for c in self.short_name)
# Pool dummy #
self.pool, self.parent = self, self
# Second init #
self.loaded = False
def __init__(self, json_path, out_dir):
# Attributes #
self.out_dir = out_dir
self.json_path = json_path
# Parse #
self.info = load_json_path(self.json_path)
# Basic #
self.account = self.info['uppmax_id']
self.run_num = self.info['run_num']
self.run_label = self.info['run_id']
self.project_short_name = self.info['project']
self.project_long_name = self.info['project_name']
self.fwd_name = self.info['forward_reads']
self.rev_name = self.info['reverse_reads']
# Own attributes #
self.num = self.info['pool_num']
self.label = self.info['pool_id']
self.short_name = self.info['pool']
self.long_name = self.info['pool_name']
self.id_name = "run%03d-pool%02d" % (self.run_num, self.num)
# Special #
self.samples = Samples(self)
self.primers = TwoPrimers(self)
# Second init #
self.loaded = False