def run(self):
"""
First, split non-full-length (nfl) fasta files into smaller
chunks, assign nfl reads in each splitted fasta file
into unpolished isoform clusters and then merge all pickles
into self.nfl_all_pickle_fn.
Second, bin every 100 clusters, for each bin, call blasr,
samto5h, loadPulses, cmph5tools to create cmp.h5 files and
call quiver to polish each isoforms within each bin.
Finally, pick up good isoform clusters whose QV errors is less
than a threshold.
Save all high quality isoforms to hq_isoforms_fa|fq if they are not None
Save all low quality isoforms to lq_isoforms_fa|fq if they are not None
"""
# Create final.consensus.fa.sa
self.add_log("Generating suffix array for {f}".format(
f=self.final_consensus_sa),
level=logging.INFO)
sa_file = self.get_sa_file()
# Create input.fasta.fofn from bas_fofn
self.add_log("Creating fasta fofn from bas/bax.h5 fofn",
level=logging.INFO)
if self.fasta_fofn is None:
self.fasta_fofn = op.join(self.nfl_dir, "input.fasta.fofn")
self.add_log("bas fofn={f}".format(f=self.bas_fofn))
self.add_log("fasta fofn={f}".format(f=self.fasta_fofn))
convert_fofn_to_fasta(fofn_filename=self.bas_fofn,
out_filename=self.fasta_fofn,
fasta_out_dir=self.nfl_dir)
# Split non-full-length reads into smaller fasta files
# and save files to root_dir/nfl_00.fa, ..., .
self.add_log("Splitting {nfl} into ".format(nfl=self.nfl_fa) +
"smaller files each containing {n} reads.".format(
n=self.ice_opts.nfl_reads_per_split),
level=logging.INFO)
self._nfl_splitted_fas = splitFasta(
input_fasta=self.nfl_fa,
reads_per_split=self.ice_opts.nfl_reads_per_split,
out_dir=self.nfl_dir,
out_prefix="input.split")
msg = "Splitted files are: " + "\n".join(self._nfl_splitted_fas)
self.add_log(msg, level=logging.INFO)
# Process nfl reads in each splitted fasta.
self.add_log("IceAllPartials initiated.", level=logging.INFO)
sa_file = self.final_consensus_sa \
if op.exists(self.final_consensus_fa) else None
self.icep = IceAllPartials(root_dir=self.root_dir,
fasta_filenames=self._nfl_splitted_fas,
ref_fasta=self.final_consensus_fa,
out_pickle=self.nfl_all_pickle_fn,
sge_opts=self.sge_opts,
sa_file=sa_file,
ccs_fofn=self.ccs_fofn)
self.icep.run()
self.add_log("IceAllPartials completed.", level=logging.INFO)
self.add_log("IceQuiver initiated.", level=logging.INFO)
self.iceq = IceQuiver(root_dir=self.root_dir,
bas_fofn=self.bas_fofn,
fasta_fofn=self.fasta_fofn,
sge_opts=self.sge_opts)
self.iceq.run()
self.add_log("IceQuiver finished.", level=logging.INFO)
self.add_log("IcePostQuiver initiated.", level=logging.INFO)
self.icepq = IcePostQuiver(root_dir=self.root_dir,
hq_isoforms_fa=self.hq_isoforms_fa,
hq_isoforms_fq=self.hq_isoforms_fq,
lq_isoforms_fa=self.lq_isoforms_fa,
lq_isoforms_fq=self.lq_isoforms_fq,
use_sge=self.sge_opts.use_sge,
quit_if_not_done=False)
self.icepq.run()
self.add_log("IcePostQuiver finished.", level=logging.INFO)
