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, barcode_map=None):
VariantSeqLib.__init__(self, config)
BarcodeSeqLib.__init__(self, config, barcodevariant=True)
try:
if 'map file' in config['barcodes']:
self.barcode_map = BarcodeMap(config['barcodes']['map file'])
else:
self.barcode_map = None
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)
if self.barcode_map is None: # not in local config
if barcode_map is None: # not provided on object creation
raise EnrichError("Barcode map not specified", self.name)
else:
self.barcode_map = barcode_map
self.counts['barcodes_unmapped'] = None
self.filter_unmapped = True
def __init__(self, config, barcode_map=None):
VariantSeqLib.__init__(self, config)
BarcodeSeqLib.__init__(self, config, barcodevariant=True)
try:
if 'map file' in config['barcodes']:
self.barcode_map = BarcodeMap(config['barcodes']['map file'])
else:
self.barcode_map = None
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)
if self.barcode_map is None: # not in local config
if barcode_map is None: # not provided on object creation
raise EnrichError("Barcode map not specified", self.name)
else:
self.barcode_map = barcode_map
self.counts['barcodes_unmapped'] = None
self.filter_unmapped = True
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:
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)
