def __init__(self, config, parent=True):
if parent:
SeqLib.__init__(self, config)
self.wt_dna = None
self.wt_protein = None
self.aligner = None
self.aligner_cache = None
try:
self.set_wt(config['wild type']['sequence'],
coding=config['wild type']['coding'])
if 'align variants' in config:
if config['align variants']:
self.aligner = Aligner()
self.aligner_cache = dict()
except KeyError as key:
raise EnrichError("Missing required config value '{key}'".format(key),
self.name)
if 'reference offset' in config['wild type']:
try:
self.reference_offset = int(config['wild type']
['reference offset'])
except ValueError:
raise EnrichError("Invalid reference offset value", self.name)
else:
self.reference_offset = 0
self.df_dict['variants'] = None
def __init__(self, config, parent=True):
if parent:
SeqLib.__init__(self, config)
self.wt_dna = None
self.wt_protein = None
self.aligner = None
self.aligner_cache = None
try:
self.set_wt(config['wild type']['sequence'],
coding=config['wild type']['coding'])
if 'align variants' in config:
if config['align variants']:
self.aligner = Aligner()
self.aligner_cache = dict()
except KeyError as key:
raise EnrichError(
"Missing required config value '{key}'".format(key), self.name)
if 'reference offset' in config['wild type']:
try:
self.reference_offset = int(
config['wild type']['reference offset'])
except ValueError:
raise EnrichError("Invalid reference offset value", self.name)
else:
self.reference_offset = 0
self.df_dict['variants'] = 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, 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