def load(self):
"""A second __init__ that is delayed, solves some circular references"""
# Automatic paths #
self.base_dir = self.out_dir + self.id_name + '/'
self.p = AutoPaths(self.base_dir, self.all_paths)
# Make an alias to the json #
self.p.info_json.link_from(self.json_path, safe=True)
# Children #
self.samples.load()
# Raw file pairs #
self.fwd_path = home + "ILLUMITAG/INBOX/%s/%s/%s" % (self.run.label, self.label, self.info['forward_reads'])
self.rev_path = home + "ILLUMITAG/INBOX/%s/%s/%s" % (self.run.label, self.label, self.info['reverse_reads'])
self.fwd = FASTQ(self.fwd_path)
self.rev = FASTQ(self.rev_path)
self.fastq = PairedFASTQ(self.fwd.path, self.rev.path, self)
# Barcode length #
self.bar_len = self.samples.bar_len
# Make Outcomes #
self.no_barcodes = NoBarcode(self)
self.one_barcodes = OneBarcode(self)
self.same_barcodes = SameBarcode(self)
self.bad_barcodes = BadBarcode(self)
self.good_barcodes = GoodBarcode(self)
self.outcomes = (self.good_barcodes, self.no_barcodes, self.one_barcodes, self.same_barcodes, self.bad_barcodes)
self.children = self.outcomes
# The good reads #
self.quality_reads = QualityReads(self.good_barcodes.assembled.good_primers.len_filtered, self)
self.fractions = Fractions(self)
# Runner #
self.runner = PoolRunner(self)
# Graphs #
self.graphs = [getattr(pool_plots, cls_name)(self) for cls_name in pool_plots.__all__]
# Loaded #
self.loaded = True
# Return self for convenience #
return self
