def __init__(self, path, parent):
# Save parent #
self.parent, self.outcome = parent, parent
self.samples = parent.samples
# Extra #
self.pool = self.outcome.parent
self.samples = self.pool.samples
self.primers = self.pool.primers
# Load #
self.load()
# Auto paths #
self.p = AutoPaths(self.base_dir, self.all_paths)
# All primer outcomes #
self.good_primers = GoodPrimers(self)
self.wrong_primers = WrongPrimers(self)
self.only_fwd_primers = OnlyFwdPrimers(self)
self.only_rev_primers = OnlyRevPrimers(self)
self.no_primers = NoPrimers(self)
# Group them #
self.children = (self.good_primers, self.wrong_primers, self.only_fwd_primers, self.only_rev_primers, self.no_primers)
class AssembleGroup(object):
"""A bunch of sequences all having the same type of assembly outcome
(and barcode outcome)"""
primer_mismatches = 1
def __iter__(self): return iter(self.children)
def __repr__(self): return '<%s object of %s>' % (self.__class__.__name__, self.parent)
def __len__(self): return self.count
def __ne__(self, other): return not self.__eq__(other)
def __init__(self, path, parent):
# Save parent #
self.parent, self.outcome = parent, parent
self.samples = parent.samples
# Extra #
self.pool = self.outcome.parent
self.samples = self.pool.samples
self.primers = self.pool.primers
# Load #
self.load()
# Auto paths #
self.p = AutoPaths(self.base_dir, self.all_paths)
# All primer outcomes #
self.good_primers = GoodPrimers(self)
self.wrong_primers = WrongPrimers(self)
self.only_fwd_primers = OnlyFwdPrimers(self)
self.only_rev_primers = OnlyRevPrimers(self)
self.no_primers = NoPrimers(self)
# Group them #
self.children = (self.good_primers, self.wrong_primers, self.only_fwd_primers, self.only_rev_primers, self.no_primers)
@property
def first(self): return self.children[0]
@property
def flipped_iterator(self):
for r in self.parse_barcodes():
if r.first.set == 'R' or r.last.set == 'F': yield reverse_compl_with_name(r.read)
else: yield r.read
def flip_reads(self):
self.flipped_reads.write(self.flipped_iterator)
def dont_flip_reads(self):
self.flipped_reads.link_from(self.path)
def make_primer_groups(self):
for g in self.children: g.create()
for r in self.flipped_reads.parse_primers(mismatches=self.primer_mismatches):
if r.fwd_start_pos is not None and r.rev_start_pos is not None:
if r.fwd_start_pos < 70 and r.rev_start_pos > -70: self.good_primers.add_seq(r.read)
else: self.wrong_primers.add_seq(r.read)
elif r.fwd_start_pos: self.only_fwd_primers.add_seq(r.read)
elif r.rev_start_pos: self.only_rev_primers.add_seq(r.read)
else: self.no_primers.add_seq(r.read)
for g in self.children: g.close()
@property_cached
def primer_positions(self):
# Count positions #
all_fwd_pos, all_rev_pos = Counter(), Counter()
for r in self.flipped_reads.parse_primers():
if r.fwd_pos is not None: all_fwd_pos.update((r.fwd_pos,))
if r.rev_pos is not None: all_rev_pos.update((r.rev_pos,))
# Return results #
return all_fwd_pos, all_rev_pos
def discard_reads_with_n(self):
for g in self.children: g.n_filter()