def __init__(self, config):
VariantSeqLib.__init__(self, config)
try:
self.forward = config['fastq']['forward']
self.reverse = config['fastq']['reverse']
self.fwd_start = int(config['overlap']['forward start'])
self.rev_start = int(config['overlap']['reverse start'])
self.overlap_length = int(config['overlap']['length'])
self.trim = config['overlap']['overlap only']
self.max_overlap_mismatches = int(config['overlap']
['max mismatches'])
if 'merge failure' in config['filters']:
raise EnrichError("'merge failure' is not user-configurable",
self.name)
self.set_filters(config['filters'], {'remove unresolvable' : False,
'min quality' : 0,
'avg quality' : 0,
'max mutations' : len(self.wt_dna),
'chastity' : False,
'merge failure' : True})
except KeyError as key:
raise EnrichError("Missing required config value %s" % key,
self.name)
except ValueError as value:
raise EnrichError("Invalid parameter value %s" % value, self.name)
try:
check_fastq(self.forward)
check_fastq(self.reverse)
except IOError as fqerr:
raise EnrichError("FASTQ file error: %s" % fqerr, self.name)
def __init__(self, config):
VariantSeqLib.__init__(self, config)
try:
if 'forward' in config['fastq'] and 'reverse' in config['fastq']:
raise EnrichError("Multiple FASTQ files specified", self.name)
elif 'forward' in config['fastq']:
self.reads = config['fastq']['forward']
self.revcomp_reads = False
elif 'reverse' in config['fastq']:
self.reads = config['fastq']['reverse']
self.revcomp_reads = True
else:
raise KeyError("'forward' or 'reverse'")
self.set_filters(config['filters'], {'min quality' : 0,
'avg quality' : 0,
'chastity' : False,
'max mutations' : len(self.wt_dna)})
except KeyError as key:
raise EnrichError("missing required config value: %s" % key, self.name)
try:
check_fastq(self.reads)
except IOError as fqerr:
raise EnrichError("FASTQ file error: %s" % fqerr, self.name)
def __init__(self, config):
VariantSeqLib.__init__(self, config)
try:
self.forward = config['fastq']['forward']
self.reverse = config['fastq']['reverse']
self.fwd_start = int(config['overlap']['forward start'])
self.rev_start = int(config['overlap']['reverse start'])
self.overlap_length = int(config['overlap']['length'])
self.trim = config['overlap']['overlap only']
self.max_overlap_mismatches = int(config['overlap']
['max mismatches'])
if 'merge failure' in config['filters']:
raise EnrichError("'merge failure' is not user-configurable",
self.name)
self.set_filters(config['filters'], {'remove unresolvable' : False,
'min quality' : 0,
'avg quality' : 0,
'max mutations' : len(self.wt_dna),
'chastity' : False,
'merge failure' : True})
except KeyError as key:
raise EnrichError("Missing required config value %s" % key,
self.name)
except ValueError as value:
raise EnrichError("Invalid parameter value %s" % value, self.name)
try:
check_fastq(self.forward)
check_fastq(self.reverse)
except IOError as fqerr:
raise EnrichError("FASTQ file error: %s" % fqerr, self.name)
def __init__(self, config):
VariantSeqLib.__init__(self, config)
try:
if 'forward' in config['fastq'] and 'reverse' in config['fastq']:
raise EnrichError("Multiple FASTQ files specified", self.name)
elif 'forward' in config['fastq']:
self.reads = config['fastq']['forward']
self.revcomp_reads = False
elif 'reverse' in config['fastq']:
self.reads = config['fastq']['reverse']
self.revcomp_reads = True
else:
raise KeyError("'forward' or 'reverse'")
self.set_filters(
config['filters'], {
'min quality': 0,
'avg quality': 0,
'chastity': False,
'max mutations': len(self.wt_dna)
})
except KeyError as key:
raise EnrichError("missing required config value: %s" % key,
self.name)
try:
check_fastq(self.reads)
except IOError as fqerr:
raise EnrichError("FASTQ file error: %s" % fqerr, self.name)
def __init__(self, config, barcodevariant=False):
self.barcodevariant = barcodevariant
if not self.barcodevariant:
SeqLib.__init__(self, config)
try:
if 'forward' in config['fastq'] and 'reverse' in config['fastq']:
raise EnrichError("Multiple FASTQ files specified", self.name)
elif 'forward' in config['fastq']:
self.reads = config['fastq']['forward']
self.revcomp_reads = False
elif 'reverse' in config['fastq']:
self.reads = config['fastq']['reverse']
self.revcomp_reads = True
else:
raise KeyError("'forward' or 'reverse'")
if 'start' in config['fastq']:
self.bc_start = config['fastq']['start']
else:
self.bc_start = 1
if 'length' in config['fastq']:
self.bc_length = config['fastq']['length']
else:
self.bc_length = 2147483647 # longer than any read... for now
if 'min count' in config['barcodes']:
self.min_count = config['barcodes']['min count']
else:
self.min_count = 0
self.set_filters(config['filters'], {
'min quality': 0,
'avg quality': 0,
'chastity': False
})
except KeyError as key:
raise EnrichError(
"Missing required config value {key}".format(key=key),
self.name)
try:
check_fastq(self.reads)
except IOError as fqerr:
raise EnrichError("FASTQ file error: {error}".format(error=fqerr),
self.name)
self.df_dict['barcodes'] = None
if self.min_count > 0:
self.df_dict['barcodes_low_abundance'] = None
def __init__(self, config, barcodevariant=False):
self.barcodevariant = barcodevariant
if not self.barcodevariant:
SeqLib.__init__(self, config)
try:
if 'forward' in config['fastq'] and 'reverse' in config['fastq']:
raise EnrichError("Multiple FASTQ files specified", self.name)
elif 'forward' in config['fastq']:
self.reads = config['fastq']['forward']
self.revcomp_reads = False
elif 'reverse' in config['fastq']:
self.reads = config['fastq']['reverse']
self.revcomp_reads = True
else:
raise KeyError("'forward' or 'reverse'")
if 'start' in config['fastq']:
self.bc_start = config['fastq']['start']
else:
self.bc_start = 1
if 'length' in config['fastq']:
self.bc_length = config['fastq']['length']
else:
self.bc_length = 2147483647 # longer than any read... for now
if 'min count' in config['barcodes']:
self.min_count = config['barcodes']['min count']
else:
self.min_count = 0
self.set_filters(config['filters'], {'min quality' : 0,
'avg quality' : 0,
'chastity' : False})
except KeyError as key:
raise EnrichError("Missing required config value {key}".format(key=key), self.name)
try:
check_fastq(self.reads)
except IOError as fqerr:
raise EnrichError("FASTQ file error: {error}".format(error=fqerr), self.name)
self.df_dict['barcodes'] = None
if self.min_count > 0:
self.df_dict['barcodes_low_abundance'] = None
def __init__(self, config, parent=True):
if parent:
SeqLib.__init__(self, config)
try:
if "forward" in config["fastq"] and "reverse" in config["fastq"]:
raise EnrichError("Multiple FASTQ files specified", self.name)
elif "forward" in config["fastq"]:
self.reads = config["fastq"]["forward"]
self.revcomp_reads = False
elif "reverse" in config["fastq"]:
self.reads = config["fastq"]["reverse"]
self.revcomp_reads = True
else:
raise KeyError("'forward' or 'reverse'")
if "start" in config["fastq"]:
self.bc_start = config["fastq"]["start"]
else:
self.bc_start = 1
if "length" in config["fastq"]:
self.bc_length = config["fastq"]["length"]
else:
self.bc_length = 2147483647 # longer than any read... for now
if "min count" in config["barcodes"]:
self.min_count = config["barcodes"]["min count"]
else:
self.min_count = 0
self.set_filters(config["filters"], {"min quality": 0, "avg quality": 0, "chastity": False})
except KeyError as key:
raise EnrichError("Missing required config value %s" % key, self.name)
try:
check_fastq(self.reads)
except IOError as fqerr:
raise EnrichError("FASTQ file error: %s" % fqerr, self.name)
self.counts["barcodes"] = None
