def __init__(self, parent):
# Save parent #
self.parent, self.pool = parent, parent
self.samples = parent.samples
# Paths #
self.base_dir = self.pool.p.groups_dir + self.short_name + '/'
self.p = AutoPaths(self.base_dir, self.all_paths)
# Super #
self.fwd_path = self.p.fwd_fastq
self.rev_path = self.p.rev_fastq
self.gzipped = True if self.fwd_path.endswith('gz') else False
# Compatible with fasta module #
self.fwd = FASTQ(self.fwd_path)
self.rev = FASTQ(self.rev_path)
# Add assembly files #
self.assembled = Assembled('', self)
self.unassembled = Unassembled('', self)
self.children = (self.assembled, self.unassembled)
self.first = self.assembled
# Graphs #
self.graphs = [getattr(outcome_plots, cls_name)(self) for cls_name in outcome_plots.__all__]
def __init__(self, parent):
# Save parent #
self.parent, self.pool = parent, parent
self.samples = parent.samples
# Paths #
self.base_dir = self.pool.p.groups_dir + self.short_name + '/'
self.p = AutoPaths(self.base_dir, self.all_paths)
# Super #
self.fwd_path = self.p.fwd_fastq
self.rev_path = self.p.rev_fastq
self.gziped = True if self.fwd_path.endswith('gz') else False
# Add assembly files #
self.assembled = Assembled(self)
self.unassembled = Unassembled(self)
self.children = (self.assembled, self.unassembled)
self.first = self.assembled
# Graphs #
self.graphs = [
getattr(outcome_plots, cls_name)(self)
for cls_name in outcome_plots.__all__
]
class BarcodeGroup(PairedFASTQ):
"""A bunch of sequences all having the same type of barcode outcome"""
short_name = "generic_barcode_outcome"
all_paths = """
/fwd.fastq
/rev.fastq
/graphs/
/assembled/
/unassembled/
"""
def __iter__(self): return iter(self.children)
def __repr__(self): return '<%s object of pool %i>' % (self.__class__.__name__, self.pool.num)
def __init__(self, parent):
# Save parent #
self.parent, self.pool = parent, parent
self.samples = parent.samples
# Paths #
self.base_dir = self.pool.p.groups_dir + self.short_name + '/'
self.p = AutoPaths(self.base_dir, self.all_paths)
# Super #
self.fwd_path = self.p.fwd_fastq
self.rev_path = self.p.rev_fastq
self.gzipped = True if self.fwd_path.endswith('gz') else False
# Compatible with fasta module #
self.fwd = FASTQ(self.fwd_path)
self.rev = FASTQ(self.rev_path)
# Add assembly files #
self.assembled = Assembled('', self)
self.unassembled = Unassembled('', self)
self.children = (self.assembled, self.unassembled)
self.first = self.assembled
# Graphs #
self.graphs = [getattr(outcome_plots, cls_name)(self) for cls_name in outcome_plots.__all__]
def join(self):
"""Uses pandaseq 2.8"""
self.assembled.remove()
command = 'pandaseq28 -T 1 -f %s -r %s -u %s -F 1> %s 2> %s'
command = command % (self.fwd_path, self.rev_path, self.unassembled.path, self.assembled.path, self.assembled.p.out)
shell_call(command) # Because it exits with status 1 https://github.com/neufeld/pandaseq/issues/40
def check_noalign_counts(self):
"""Check the sanity of pandaseq"""
assert len(self.assembled) + len(self.unassembled) + self.assembled.stats['lowqual'] == len(self)
assert self.assembled.stats['noalign'] == self.unassembled.count
def barcode_fastqc(self):
sh.fastqc(self.fwd_path, '-q')
os.remove(os.path.splitext(self.fwd_path)[0] + '_fastqc.zip')
sh.fastqc(self.rev_path, '-q')
os.remove(os.path.splitext(self.rev_path)[0] + '_fastqc.zip')
def assembly_fastqc(self):
sh.fastqc(self.assembled.path, '-q')
os.remove(os.path.splitext(self.assembled.path)[0] + '_fastqc.zip')
def make_outcome_plots(self):
for graph in self.graphs: graph.plot()
