def list_samples(self):
sample_names = self.samples_config.list_sample_names()
samples = []
for name in sample_names:
mates = [Mate.from_dict(mate) for mate in self.samples_config.list_mates_for_sample(name)]
samples.append(Sample(mates, name))
return samples
def get_sample_by_name(self, name):
mates = self.samples_config.list_mates_for_sample(name)
mates = [Mate.from_dict(mate) for mate in mates]
sample = Sample(mates, name)
return sample
def get_mate_by_name(self, name):
mate_dict = self.samples_config.get_mate_by_name(name)
return Mate.from_dict(mate_dict)
def list_project_mates(self):
mates = self.samples_config.list_mates()
return [Mate.from_dict(mate) for mate in mates]
def list_mates_to_align(self):
cnfg = SamplesConfig("Config/samples_config.yaml")
mates_to_align = [Mate.from_dict(mate) for mate in cnfg.list_mates()]
mates_to_align = filter(lambda x: x.align, mates_to_align)
return mates_to_align