def build_uc_from_partial_daligner(input_fastq, ref_fasta, out_pickle,
ccs_fofn=None,
done_filename=None, use_finer_qv=False, cpus=24, no_qv_or_aln_checking=True):
"""
Given an input_fasta file of non-full-length (partial) reads and
(unpolished) consensus isoforms sequences in ref_fasta, align reads to
consensus isoforms using BLASR, and then build up a mapping between
consensus isoforms and reads (i.e., assign reads to isoforms).
Finally, save
{isoform_id: [read_ids],
nohit: set(no_hit_read_ids)}
to an output pickle file.
ccs_fofn --- If None, assume no quality value is available,
otherwise, use QV from ccs_fofn.
"""
input_fastq = realpath(input_fastq)
input_fasta = input_fastq[:input_fastq.rfind('.')] + '.fasta'
ice_fq2fa(input_fastq, input_fasta)
ref_fasta = realpath(ref_fasta)
out_pickle = realpath(out_pickle)
output_dir = os.path.dirname(out_pickle)
daligner_sensitive_mode, _low, _high, _ignore5, _ignore3, _ece_min_len = get_daligner_sensitivity_setting(ref_fasta, is_fasta=True)
# DB should always be already converted
ref_obj = DazzIDHandler(ref_fasta, True)
input_obj = DazzIDHandler(input_fasta, False)
# ice_partial is already being called through qsub, so run everything local!
runner = DalignerRunner(input_fasta, ref_fasta, is_FL=False, same_strand_only=False, \
query_converted=True, db_converted=True, query_made=False, \
db_made=True, use_sge=False, cpus=cpus, sge_opts=None)
las_filenames, las_out_filenames = runner.runHPC(min_match_len=_low, output_dir=output_dir, sensitive_mode=daligner_sensitive_mode)
if no_qv_or_aln_checking:
# not using QVs or alignment checking!
# this probqv is just a DUMMY to pass to daligner_against_ref, which won't be used
logging.info("Not using QV for partial_uc. Loading dummy QV.")
probqv = ProbFromModel(.01, .07, .06)
else:
# if ccs_fofn is None:
# logging.info("Loading probability from model (0.01,0.07,0.06)")
# probqv = ProbFromModel(.01, .07, .06)
# else:
start_t = time.time()
probqv = ProbFromFastq(input_fastq)
logging.info("Loading QVs from {fq} took {s} secs".format(fq=input_fastq, s=time.time()-start_t))
# --------- comment out below since we are just using FASTQ / BAM
# if use_finer_qv:
# probqv = ProbFromQV(input_fofn=ccs_fofn, fasta_filename=input_fasta)
# logging.info("Loading QVs from {i} + {f} took {s} secs".format(f=ccs_fofn, i=input_fasta,\
# s=time.time()-start_t))
# else:
# input_fastq = input_fasta[:input_fasta.rfind('.')] + '.fastq'
# logging.info("Converting {i} + {f} --> {fq}".format(i=input_fasta, f=ccs_fofn, fq=input_fastq))
# ice_fa2fq(input_fasta, ccs_fofn, input_fastq)
# probqv = ProbFromFastq(input_fastq)
# logging.info("Loading QVs from {fq} took {s} secs".format(fq=input_fastq, s=time.time()-start_t))
# print >> sys.stderr, "Loading QVs from {fq} took {s} secs".format(fq=input_fastq, s=time.time()-start_t)
logging.info("Calling dalign_against_ref ...")
partial_uc = {} # Maps each isoform (cluster) id to a list of reads
# which can map to the isoform
seen = set() # reads seen
logging.info("Building uc from DALIGNER hits.")
for las_out_filename in las_out_filenames:
start_t = time.time()
hitItems = dalign_against_ref(input_obj, ref_obj, las_out_filename,
is_FL=False,
sID_starts_with_c=True,
qver_get_func=probqv.get_smoothed,
qvmean_get_func=probqv.get_mean,
ece_penalty=1,
ece_min_len=_ece_min_len,
same_strand_only=False,
no_qv_or_aln_checking=no_qv_or_aln_checking,
max_missed_start=_ignore5,
max_missed_end=_ignore3)
for h in hitItems:
if h.ece_arr is not None:
if h.cID not in partial_uc:
partial_uc[h.cID] = set()
partial_uc[h.cID].add(h.qID)
seen.add(h.qID)
logging.info("processing {0} took {1} sec".format(las_out_filename, time.time()-start_t))
print >> sys.stderr, "processing {0} took {1} sec".format(las_out_filename, time.time()-start_t)
for k in partial_uc:
partial_uc[k] = list(partial_uc[k])
allhits = set(r.name.split()[0] for r in FastaReader(input_fasta))
logging.info("Counting reads with no hit.")
nohit = allhits.difference(seen)
logging.info("Dumping uc to a pickle: {f}.".format(f=out_pickle))
with open(out_pickle, 'w') as f:
dump({'partial_uc': partial_uc, 'nohit': nohit}, f)
done_filename = realpath(done_filename) if done_filename is not None \
else out_pickle + '.DONE'
logging.debug("Creating {f}.".format(f=done_filename))
touch(done_filename)
# remove all the .las and .las.out filenames
for file in las_filenames:
os.remove(file)
for file in las_out_filenames:
os.remove(file)
def run(self):
"""Call ICE to cluster consensus isoforms."""
self.add_log("Start to run cluster.", level=logging.INFO)
if self.ice_opts.targeted_isoseq:
first_split = 1000
self.ice_opts.flnc_reads_per_split = 10000
self.add_log("targeted_isoseq: further splitting JUST first split to 1000. Changing flnc_reads_per_split=10000.")
else:
first_split = None
# Split flnc_fa into smaller files and save files to _flnc_splitted_fas.
self.add_log("Splitting {flnc} into ".format(flnc=self.flnc_fa) +
"smaller files each containing {n} reads.".format(
n=self.ice_opts.flnc_reads_per_split),
level=logging.INFO)
self._flnc_splitted_fqs = splitFastq(
input_fastq=self.flnc_fa,
reads_per_split=self.ice_opts.flnc_reads_per_split,
out_dir=self.root_dir,
out_prefix="input.split",
first_split=first_split)
self.add_log("Splitted files are: " +
"\n".join(self._flnc_splitted_fqs),
level=logging.INFO)
firstSplit_fq = self._flnc_splitted_fqs[0]
firstSplit_fa = firstSplit_fq[:firstSplit_fq.rfind('.')] + '.fasta'
ice_fq2fa(firstSplit_fq, firstSplit_fa)
# -------- commenting out below because we already have FASTQ!
#firstSplit = self._flnc_splitted_fas[0]
#firstSplit_fq = firstSplit[:firstSplit.rfind('.')] + '.fastq'
#self.add_log("Converting first split file {0} + {1} into fastq\n".format(\
# firstSplit, self.ccs_fofn), level=logging.INFO)
## Convert this into FASTQ
#ice_fa2fq(firstSplit, self.ccs_fofn, firstSplit_fq)
#
## Set up probabbility and quality value model
#if self.ice_opts.use_finer_qv:
# self._setProbQV_ccs(self.ccs_fofn, firstSplit)
#else:
# self._setProbQV_fq(firstSplitFq=firstSplit_fq)
self._setProbQV_fq(firstSplitFq=firstSplit_fq)
# Initialize cluster by clique
if os.path.exists(self.initPickleFN):
self.add_log("Reading existing uc pickle: {0}".format(self.initPickleFN), level=logging.INFO)
with open(self.initPickleFN) as f:
uc = cPickle.load(f)
else:
self.add_log("Finding maximal cliques: initializing IceInit.",
level=logging.INFO)
self.iceinit = IceInit(readsFa=firstSplit_fa,
qver_get_func=self._probqv.get_smoothed,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts,
qvmean_get_func=self._probqv.get_mean)
uc = self.iceinit.uc
# Dump uc to a file
self.add_log("Dumping initial clusters to {f}".format(
f=self.initPickleFN), level=logging.INFO)
with open(self.initPickleFN, 'w') as f:
cPickle.dump(uc, f)
# Run IceIterative.
self.add_log("Iterative clustering: initializing IceIterative.",
level=logging.INFO)
#self.add_log("In Cluster. DEBUG: Calling Cluster with {0} {1} {2} ".format(self.bas_fofn, self.ccs_fofn, self.fasta_fofn))
self.icec = IceIterative(
fasta_filename=firstSplit_fa,
fastq_filename=firstSplit_fq,
fastq_filenames_to_add=self._flnc_splitted_fqs[1:],
all_fasta_filename=self.flnc_fa,
ccs_fofn=self.ccs_fofn,
root_dir=self.root_dir,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts,
uc=uc,
probQV=self._probqv,
use_ccs_qv=self.ice_opts.use_finer_qv)
self.add_log("IceIterative log: {f}.".format(f=self.icec.log_fn))
self.icec.run()
self.add_log("IceIterative completed.", level=logging.INFO)
# IceIterative done, write predicted (unplished) consensus isoforms
# to an output fasta
self.add_log("Creating a link to unpolished consensus isoforms.")
ln(self.icec.final_consensus_fa, self.out_fa)
#self.add_log("In Cluster. DEBUG: End Cluster with {0} {1} {2} ".format(self.bas_fofn, self.ccs_fofn, self.fasta_fofn))
# Call quiver to polish predicted consensus isoforms.
if self.ice_opts.quiver is not True:
self.add_log("Creating a link to cluster report.",
level=logging.INFO)
ln(src=self.icec.report_fn, dst=self.report_fn)
# Summarize cluster and write to summary_fn.
self.write_summary(summary_fn=self.summary_fn,
isoforms_fa=self.out_fa)
else: # self.ice_opts.quiver is True
self.add_log("Polishing clusters: initializing IcePolish.",
level=logging.INFO)
#self.add_log("In Cluster. DEBUG: Calling Polish with {0} {1} {2} ".format(self.bas_fofn, self.ccs_fofn, self.fasta_fofn))
self.pol = Polish(root_dir=self.root_dir,
nfl_fa=self.nfl_fa,
bas_fofn=self.bas_fofn,
ccs_fofn=self.ccs_fofn,
fasta_fofn=self.fasta_fofn,
ice_opts=self.ice_opts,
sge_opts=self.sge_opts,
ipq_opts=self.ipq_opts,
nfl_reads_per_split=self.nfl_reads_per_split)
self.add_log("IcePolish log: {f}.".format(f=self.pol.log_fn),
level=logging.INFO)
self.pol.run()
self.add_log("IcePolish completed.", level=logging.INFO)
# cluster report
self.add_log("Creating a link to cluster report.",
level=logging.INFO)
ln(src=self.pol.iceq.report_fn, dst=self.report_fn)
# Summarize cluster & polish and write to summary_fn.
self.write_summary(summary_fn=self.summary_fn,
isoforms_fa=self.out_fa,
hq_fa=self.pol.icepq.quivered_good_fa,
lq_fa=self.pol.icepq.quivered_bad_fa)
# Create log file.
self.close_log()
return 0