def sra_line(self): """Will generate the corresponding entry for SRA submission""" # accession line = [self.s.info['bioproject']] line += [self.s.info['biosample']] # name line += [self.s.short_name] line += [self.s.short_name] # description machine = 'Illumina MiSeq' if 'machine' not in self.s.__dict__ else self.s.machine desc = "Soda lake '%s' (code %s) sampled on %s and run on a %s" desc += " -- run number %i, pool number %i, barcode number %i." line += [desc % (self.s.info['real_name'][0], self.s.short_name, self.s.info['date'], machine, self.s.pool.run_num, self.s.pool.num, self.s.num)] # library_strategy line += [default_sra['library_strategy']] line += [default_sra['library_source']] line += [default_sra['library_selection']] line += [default_sra['library_layout']] line += [default_sra['platform']] line += [default_sra['instrument_model']] # design_description line += [self.s.pool.info['design_description']] # reference_genome_assembly line += ['', ''] # forward_read_length line += [self.forward_read_length, self.reverse_read_length] # forward line += [default_sra['forward_filetype'], self.base_name.format("forward")] line += [md5sum(self.s.p.raw_forward_gz)] # reverse line += [default_sra['reverse_filetype'], self.base_name.format("reverse")] line += [md5sum(self.s.p.raw_reverse_gz)] # return return line
def run_parameters(self): """Generate the 'run' required parameters for submitting this sample to ENA""" return { 'unique_name': "run" + self.s.name, 'experiment_name': "experiment_" + self.s.short_name, 'fwd_filename': self.base_name.format('forward'), 'fwd_checksum': md5sum(self.s.p.raw_forward_gz), 'rev_filename': self.base_name.format('reverse'), 'rev_checksum': md5sum(self.s.p.raw_reverse_gz), }
def md5(self): """Return the md5 checksum.""" return md5sum(self.path)
def rev_md5(self): return md5sum(self.s.p.raw_sff) ############################################################################### class Pyrosample(object):
def fwd_md5(self): return md5sum(self.s.p.raw_sff) @property