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 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