Exemple #1
0
 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
Exemple #2
0
 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
Exemple #3
0
 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