class GoodPrimers(PrimerGroup):
"""Both primers found at right place"""
short_name = 'good_primers'
all_paths = PrimerGroup.all_paths + """
/
/chimeras_ref/
/chimeras_denovo/
"""
def load(self):
if self.parent == 'assembled':
self.uchime_ref = UchimeRef(self.trimmed_barcodes.path, self.p.chimeras_ref_dir, self)
self.uchime_denovo = UchimeDenovo(self.trimmed_barcodes.path, self.p.chimeras_denovo_dir, self)
def check_chimeras(self):
# Only assembled sequences #
if self.parent != 'assembled': return
# Message #
message = "----> Checking pool %i %s for chimeras"
print Color.l_ylw + message % (self.parent.parent.pool.num, self.parent.parent.short_name) + Color.end
sys.stdout.flush()
# Check empty #
if not self.trimmed_barcodes:
print Color.l_ylw + 'No chimeras to check for %s (empty set)' % (self,) + Color.end
sys.stdout.flush()
return
# Call #
self.uchime_ref.check()
self.uchime_denovo.check()
class GoodPrimers(PrimerGroup):
"""Both primers found at right place"""
short_name = 'good_primers'
all_paths = PrimerGroup.all_paths + """
/
/chimeras_ref/
/chimeras_denovo/
"""
def load(self):
if self.parent == 'assembled':
self.uchime_ref = UchimeRef(self.trimmed_barcodes.path, self.p.chimeras_ref_dir, self)
self.uchime_denovo = UchimeDenovo(self.trimmed_barcodes.path, self.p.chimeras_denovo_dir, self)
def check_chimeras(self):
# Only assembled sequences #
if self.parent != 'assembled': return
# Message #
message = "----> Checking pool %i %s for chimeras"
print Color.l_ylw + message % (self.parent.parent.pool.num, self.parent.parent.short_name) + Color.end
sys.stdout.flush()
# Check empty #
if not self.trimmed_barcodes:
print Color.l_ylw + 'No chimeras to check for %s (empty set)' % (self,) + Color.end
sys.stdout.flush()
return
# Call #
self.uchime_ref.check()
self.uchime_denovo.check()
def __init__(self, parent, base_dir, lower_bound, upper_bound):
# Save parent #
self.parent, self.fractions = parent, parent
# Auto paths #
self.base_dir = base_dir
self.p = AutoPaths(self.base_dir, self.all_paths)
# Bounds #
self.lower_bound = lower_bound
self.upper_bound = upper_bound
# Size fractions #
self.reads = FASTA(self.p.reads_fasta)
self.refere = UchimeRef(self.p.reads, self.p.refere_dir, self)
self.denovo = UchimeDenovo(self.p.reads, self.p.denovo_dir, self)
# Classification #
self.rdp = SimpleRdpTaxonomy(self.reads, self.p.rdp_dir)
self.crest = SimpleCrestTaxonomy(self.reads, self.p.crest_dir)
class Fraction(object):
"""One size fraction from the quality reads."""
all_paths = """
/reads.fasta
/refere/
/denovo/
/rdp/
/crest/
"""
def __init__(self, parent, base_dir, lower_bound, upper_bound):
# Save parent #
self.parent, self.fractions = parent, parent
# Auto paths #
self.base_dir = base_dir
self.p = AutoPaths(self.base_dir, self.all_paths)
# Bounds #
self.lower_bound = lower_bound
self.upper_bound = upper_bound
# Size fractions #
self.reads = FASTA(self.p.reads_fasta)
self.refere = UchimeRef(self.p.reads, self.p.refere_dir, self)
self.denovo = UchimeDenovo(self.p.reads, self.p.denovo_dir, self)
# Classification #
self.rdp = SimpleRdpTaxonomy(self.reads, self.p.rdp_dir)
self.crest = SimpleCrestTaxonomy(self.reads, self.p.crest_dir)
def extract(self):
self.fractions.pool.quality_reads.only_used.extract_length(self.lower_bound, self.upper_bound, self.reads)
return self.reads
def check_chimeras(self):
self.refere.check()
self.denovo.check()
return self.refere, self.denovo
def check_classification(self):
self.rdp.assign()
class Fraction(object):
"""One size fraction from the quality reads."""
all_paths = """
/reads.fasta
/refere/
/denovo/
/rdp/
/crest/
"""
def __init__(self, parent, base_dir, lower_bound, upper_bound):
# Save parent #
self.parent, self.fractions = parent, parent
# Auto paths #
self.base_dir = base_dir
self.p = AutoPaths(self.base_dir, self.all_paths)
# Bounds #
self.lower_bound = lower_bound
self.upper_bound = upper_bound
# Size fractions #
self.reads = FASTA(self.p.reads_fasta)
self.refere = UchimeRef(self.p.reads, self.p.refere_dir, self)
self.denovo = UchimeDenovo(self.p.reads, self.p.denovo_dir, self)
# Classification #
self.rdp = SimpleRdpTaxonomy(self.reads, self.p.rdp_dir)
self.crest = SimpleCrestTaxonomy(self.reads, self.p.crest_dir)
def extract(self):
self.fractions.pool.quality_reads.only_used.extract_length(self.lower_bound, self.upper_bound, self.reads)
return self.reads
def check_chimeras(self):
self.refere.check()
self.denovo.check()
return self.refere, self.denovo
def check_classification(self):
self.rdp.assign()
def __init__(self, parent, base_dir, lower_bound, upper_bound):
# Save parent #
self.parent, self.fractions = parent, parent
# Auto paths #
self.base_dir = base_dir
self.p = AutoPaths(self.base_dir, self.all_paths)
# Bounds #
self.lower_bound = lower_bound
self.upper_bound = upper_bound
# Size fractions #
self.reads = FASTA(self.p.reads_fasta)
self.refere = UchimeRef(self.p.reads, self.p.refere_dir, self)
self.denovo = UchimeDenovo(self.p.reads, self.p.denovo_dir, self)
# Classification #
self.rdp = SimpleRdpTaxonomy(self.reads, self.p.rdp_dir)
self.crest = SimpleCrestTaxonomy(self.reads, self.p.crest_dir)
def load(self):
if self.parent == 'assembled':
self.uchime_ref = UchimeRef(self.trimmed_barcodes.path, self.p.chimeras_ref_dir, self)
self.uchime_denovo = UchimeDenovo(self.trimmed_barcodes.path, self.p.chimeras_denovo_dir, self)
def load(self):
if self.parent == 'assembled':
self.uchime_ref = UchimeRef(self.trimmed_barcodes.path, self.p.chimeras_ref_dir, self)
self.uchime_denovo = UchimeDenovo(self.trimmed_barcodes.path, self.p.chimeras_denovo_dir, self)
