def __init__(self, input_fofn, fasta_filename=None, prob_threshold=0.03, window_size=5):
self.qver = basQVcacher()
self.input_fofn = input_fofn
self.seqids = []
self.prob_threshold = prob_threshold
self.window_size = window_size
self.full_prob = None
with open(self.input_fofn) as f:
for line in f:
self.qver.add_bash5(line.strip())
if fasta_filename is not None:
self.add_seqs_from_fasta(fasta_filename)
def __init__(self, input_fofn, fasta_filename=None,
prob_threshold=.03, window_size=5):
self.qver = basQVcacher()
self.input_fofn = input_fofn
self.seqids = []
self.prob_threshold = prob_threshold
self.window_size = window_size
self.full_prob = None
with open(self.input_fofn) as f:
for line in f:
self.qver.add_bash5(line.strip())
if fasta_filename is not None:
self.add_seqs_from_fasta(fasta_filename)
def ice_fa2fq(in_fa, ccs_fofn, out_fq):
"""Convert an input FASTA file to an output FASTQ file,
reading QVs from the input ccs.h5 or ccs FOFN.
"""
qver = basQVcacher()
if ccs_fofn:
if ccs_fofn.endswith(".h5"): # Input is a ccs.h5 file not a FOFN.
qver.add_bash5(ccs_fofn)
else: # Input is a ccs FOFN containing multiple ccs.h5 files.
for ccs_fn in get_files_from_fofn(ccs_fofn):
qver.add_bash5(ccs_fn)
bas_handlers = {}
with FastaReader(in_fa) as reader, \
FastqWriter(out_fq) as writer:
for r in reader:
seqid = r.name.split(' ')[0]
movie, hn, s_e = "", "", ""
try:
movie, hn, s_e = seqid.split('/')
hn = int(hn)
except ValueError:
raise ValueError("{seqid} is not a valid CCS read".
format(seqid=seqid))
if ccs_fofn:
try:
bas_file = qver.bas_files[movie][seqid]
if bas_file not in bas_handlers:
bas_handlers[bas_file] = BasH5Reader(bas_file)
except KeyError:
raise IOError("Could not read {s} from input ccs fofn.".
format(s=seqid))
logging.debug("Getting QVs for {name} ...".format(name=r.name))
qvs = get_qv_from_bas_handler(bas_handler=bas_handlers[bas_file],
hn=hn, s_e=s_e,
qv_name="QualityValue")
else: #No quality values provided to pbtranscript.py cluster
qvs = [60]*len(r.sequence) # No information given, have strong belief in the base calls
if len(r.sequence) != len(qvs):
raise ValueError("Sequence and QVs of {r} should be the same!".
format(r=r.name))
writer.writeRecord(r.name, r.sequence, qvs)
for bas_file, bas_handler in bas_handlers.iteritems():
logging.debug("Closing {bas_file} ...".format(bas_file=bas_file))
bas_handler.close()
def ice_fa2fq(in_fa, ccs_fofn, out_fq):
"""Convert an input FASTA file to an output FASTQ file,
reading QVs from the input ccs.h5 or ccs FOFN.
"""
qver = basQVcacher()
if ccs_fofn.endswith(".h5"): # Input is a ccs.h5 file not a FOFN.
qver.add_bash5(ccs_fofn)
else: # Input is a ccs FOFN containing multiple ccs.h5 files.
for ccs_fn in get_files_from_fofn(ccs_fofn):
qver.add_bash5(ccs_fn)
bas_handlers = {}
with FastaReader(in_fa) as reader, \
FastqWriter(out_fq) as writer:
for r in reader:
seqid = r.name.split(' ')[0]
movie, hn, s_e = "", "", ""
try:
movie, hn, s_e = seqid.split('/')
hn = int(hn)
except ValueError:
raise ValueError(
"{seqid} is not a valid CCS read".format(seqid=seqid))
try:
bas_file = qver.bas_files[movie][seqid]
if bas_file not in bas_handlers:
bas_handlers[bas_file] = BasH5Reader(bas_file)
except KeyError:
raise IOError(
"Could not read {s} from input ccs fofn.".format(s=seqid))
logging.debug("Getting QVs for {name} ...".format(name=r.name))
qvs = get_qv_from_bas_handler(bas_handler=bas_handlers[bas_file],
hn=hn,
s_e=s_e,
qv_name="QualityValue")
if len(r.sequence) != len(qvs):
raise ValueError(
"Sequence and QVs of {r} should be the same!".format(
r=r.name))
writer.writeRecord(r.name, r.sequence, qvs)
for bas_file, bas_handler in bas_handlers.iteritems():
logging.debug("Closing {bas_file} ...".format(bas_file=bas_file))
bas_handler.close()
