def run(self): """Execute ice_partial.py all|split|i|merge.""" cmd = self.args.subCommand logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__), cmd=cmd, v=get_version())) cmd_str = "" try: args = self.args obj = None if cmd == "all": sge_opts = SgeOptions(unique_id=args.unique_id, use_sge=args.use_sge, max_sge_jobs=args.max_sge_jobs, blasr_nproc=args.blasr_nproc) obj = IceAllPartials( root_dir=args.root_dir, fasta_filenames=args.fasta_filenames.split(','), ref_fasta=args.ref_fasta, out_pickle=args.out_pickle, sge_opts=sge_opts, sa_file=args.sa_file, ccs_fofn=args.ccs_fofn) elif cmd == "one": # Only assign nfl reads in the given input_fasta file to isoforms obj = IcePartialOne(input_fasta=args.input_fasta, ref_fasta=args.ref_fasta, out_pickle=args.out_pickle, sa_file=args.sa_file, ccs_fofn=args.ccs_fofn, done_filename=args.done_filename, blasr_nproc=args.blasr_nproc, use_finer_qv=args.use_finer_qv) elif cmd == "split": obj = IcePartialSplit(root_dir=args.root_dir, nfl_fa=args.nfl_fa, N=args.N) elif cmd == "i": obj = IcePartialI(root_dir=args.root_dir, i=args.i, ccs_fofn=args.ccs_fofn, blasr_nproc=args.blasr_nproc) elif cmd == "merge": obj = IcePartialMerge(root_dir=args.root_dir, N=args.N) else: raise ValueError( "Unknown command passed to {f}: {cmd}.".format( f=op.basename(__file__), cmd=cmd)) cmd_str = obj.cmd_str() logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str)) obj.run() except: logging.exception("Exiting {cmd_str} with return code 1.".format( cmd_str=cmd_str)) return 1 return 0
def run(self): """Execute ice_partial.py all|split|i|merge.""" cmd = self.args.subCommand logging.info("Running {f} {cmd} v{v}.".format(f=op.basename(__file__), cmd=cmd, v=get_version())) cmd_str = "" try: args = self.args obj = None if cmd == "all": sge_opts = SgeOptions(unique_id=args.unique_id, use_sge=args.use_sge, max_sge_jobs=args.max_sge_jobs, blasr_nproc=args.blasr_nproc) obj = IceAllPartials(root_dir=args.root_dir, fasta_filenames=args.fasta_filenames.split(','), ref_fasta=args.ref_fasta, out_pickle=args.out_pickle, sge_opts=sge_opts, sa_file=args.sa_file, ccs_fofn=args.ccs_fofn) elif cmd == "one": # Only assign nfl reads in the given input_fastq file to isoforms obj = IcePartialOne(input_fastq=args.input_fastq, ref_fasta=args.ref_fasta, out_pickle=args.out_pickle, sa_file=args.sa_file, ccs_fofn=args.ccs_fofn, done_filename=args.done_filename, blasr_nproc=args.blasr_nproc, use_finer_qv=args.use_finer_qv) elif cmd == "split": obj = IcePartialSplit(root_dir=args.root_dir, nfl_fa=args.nfl_fa, N=args.N) elif cmd == "i": obj = IcePartialI(root_dir=args.root_dir, i=args.i, ccs_fofn=args.ccs_fofn, blasr_nproc=args.blasr_nproc) elif cmd == "merge": obj = IcePartialMerge(root_dir=args.root_dir, N=args.N) else: raise ValueError("Unknown command passed to {f}: {cmd}.". format(f=op.basename(__file__), cmd=cmd)) cmd_str = obj.cmd_str() logging.info("Running CMD: {cmd_str}".format(cmd_str=cmd_str)) obj.run() except: logging.exception("Exiting {cmd_str} with return code 1.". format(cmd_str=cmd_str)) return 1 return 0
class Polish(IceFiles): """Polish isoforms clusters using Quiver.""" def __init__(self, root_dir, nfl_fa, bas_fofn, ccs_fofn, ice_opts, sge_opts, hq_isoforms_fa=None, hq_isoforms_fq=None, lq_isoforms_fa=None, lq_isoforms_fq=None, fasta_fofn=None): """ root_dir --- IceFiles.root_dir, usually data/clusterOutDir nfl_fa --- non-full-length reads in fasta, e.g., isoseq_nfl.fa bas_fofn --- e.g. input.fofn of bas|bax.h5 files ccs_fofn --- e.g. reads_of_insert.fofn of ccs files. hq_isoforms_fa|fq --- polished, hiqh quality consensus isoforms in fasta|q lq_isoforms_fa|fq --- polished, low quality consensus isoforms in fasta|q """ IceFiles.__init__(self, prog_name="IcePolish", root_dir=root_dir, bas_fofn=bas_fofn, ccs_fofn=ccs_fofn, fasta_fofn=fasta_fofn) self.nfl_fa = realpath(nfl_fa) self.hq_isoforms_fa = hq_isoforms_fa self.hq_isoforms_fq = hq_isoforms_fq self.lq_isoforms_fa = lq_isoforms_fa self.lq_isoforms_fq = lq_isoforms_fq self.ice_opts = ice_opts self.sge_opts = sge_opts self.icep = None # IceAllPartials. self.iceq = None # IceQuiver self.icepq = None # IcePostQuiver self._nfl_splitted_fas = None self._validate_inputs() def _validate_inputs(self): """ Validate input directories: root_dir, and files: nfl_fa, bas_fofn, ccs_fofn. """ self.add_log("Validating inputs.") errMsg = "" if not op.exists(self.root_dir): errMsg = "Root dir {d} is not an existing directory!".\ format(d=self.root_dir) if not op.exists(self.nfl_fa): errMsg = "Failed to find non-full-length reads {f}!".\ format(f=self.nfl_fa) if not op.exists(self.bas_fofn): errMsg = "Failed to find bas fofn {f}!".format(f=self.bas_fofn) if errMsg != "": self.add_log(errMsg, level=logging.ERROR) raise ValueError(errMsg) def get_sa_file(self): """Return saffix array of final_consensus_fa.""" ret = True if not op.exists(self.final_consensus_sa): ret = build_sa(self.final_consensus_fa, self.final_consensus_sa) if ret is True: self.add_log( "Successfully created a suffix array for {f} at {sa}.".format( f=self.final_consensus_fa, sa=self.final_consensus_sa)) else: self.add_log("Failed to generate suffix array for {f}".format( f=self.final_consensus_fa), level=logging.WARNING) if op.exists(self.final_consensus_sa): return self.final_consensus_sa else: return None 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)
class Polish(IceFiles): """Polish isoforms clusters using Quiver.""" def __init__(self, root_dir, nfl_fa, bas_fofn, ccs_fofn, ice_opts, sge_opts, ipq_opts, fasta_fofn=None, nfl_reads_per_split=30000): """ root_dir --- IceFiles.root_dir, usually data/clusterOutDir nfl_fa --- non-full-length reads in fasta, e.g., isoseq_nfl.fa bas_fofn --- e.g. input.fofn of bas|bax.h5 files ccs_fofn --- e.g. reads_of_insert.fofn of ccs files. ipq_opts --- IceQuiverHQLQOptions qv_trim_5: ignore QV of n bases in the 5' end qv_trim_3: ignore QV of n bases in the 3' end hq_quiver_min_accuracy: minimum allowed quiver accuracy to mark an isoform as high quality hq_isoforms_fa|fq: polished, hiqh quality consensus isoforms in fasta|q lq_isoforms_fa|fq: polished, low quality consensus isoforms in fasta|q """ IceFiles.__init__(self, prog_name="IcePolish", root_dir=root_dir, bas_fofn=bas_fofn, ccs_fofn=ccs_fofn, fasta_fofn=fasta_fofn) #self.add_log("DEBUG: in Polish ccs_fofn is {0}".format(self.ccs_fofn)) #self.add_log("DEBUG: in Polish fasta_fofn is {0}".format(self.fasta_fofn)) #self.add_log("DEBUG: in Polish bas_fofn is {0}".format(self.bas_fofn)) self.nfl_fa = realpath(nfl_fa) self.nfl_reads_per_split = nfl_reads_per_split self.ice_opts = ice_opts self.sge_opts = sge_opts self.ipq_opts = ipq_opts self.add_log("ece_penalty: {0}, ece_min_len: {1}".format(self.ice_opts.ece_penalty, self.ice_opts.ece_min_len)) self.icep = None # IceAllPartials. self.iceq = None # IceQuiver self.icepq = None # IceQuiverPostprocess self._nfl_splitted_fas = None self.validate_inputs() def validate_inputs(self): """ Validate input directories: root_dir, and files: nfl_fa, bas_fofn, ccs_fofn. """ self.add_log("Validating inputs.") errMsg = "" if not op.exists(self.root_dir): errMsg = "Root dir {d} is not an existing directory!".\ format(d=self.root_dir) if not op.exists(self.nfl_fa): errMsg = "Failed to find non-full-length reads {f}!".\ format(f=self.nfl_fa) if not op.exists(self.bas_fofn): errMsg = "Failed to find bas fofn {f}!".format(f=self.bas_fofn) if errMsg != "": self.add_log(errMsg, level=logging.ERROR) raise ValueError(errMsg) # def get_sa_file(self): # """Return saffix array of final_consensus_fa.""" # ret = True # if not op.exists(self.final_consensus_sa): # ret = build_sa(self.final_consensus_fa, self.final_consensus_sa) # # if ret is True: # self.add_log("Successfully created a suffix array for {f} at {sa}.". # format(f=self.final_consensus_fa, # sa=self.final_consensus_sa)) # else: # self.add_log("Failed to generate suffix array for {f}".format( # f=self.final_consensus_fa), level=logging.WARNING) # if op.exists(self.final_consensus_sa): # return self.final_consensus_sa # else: # return None 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)) if op.exists(self.fasta_fofn): self.add_log("No need to run convert_fofn_to_fasta.") else: convert_fofn_to_fasta(fofn_filename=self.bas_fofn, out_filename=self.fasta_fofn, fasta_out_dir=self.nfl_dir, cpus=self.sge_opts.blasr_nproc) # 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.nfl_reads_per_split), level=logging.INFO) self._nfl_splitted_fas = splitFasta(input_fasta=self.nfl_fa, reads_per_split=self.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) # Generating dazz DB for final.consensus.fasta ref_obj = DazzIDHandler(self.final_consensus_fa, False) DalignerRunner.make_db(ref_obj.dazz_filename) msg = "Dazz DB made for: " + ref_obj.dazz_filename self.add_log(msg, level=logging.INFO) # Process nfl reads in each splitted fasta. self.add_log("Initializing IceAllPartials.", 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=None, # since we are switching to daligner, just give it as None now; remove sa_file completely later when daligner is mature (ToDo) ccs_fofn=self.ccs_fofn) self.add_log("IceAllPartials log: {f}.".format(f=self.icep.log_fn), level=logging.INFO) self.icep.run() self.add_log("IceAllPartials completed.", level=logging.INFO) self.add_log("Initializing IceQuiver.", 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.add_log("IceQuiver log: {f}.".format(f=self.iceq.log_fn), level=logging.INFO) self.iceq.run() self.add_log("IceQuiver finished.", level=logging.INFO) self.add_log("Initializing IceQuiverPostprocess.", level=logging.INFO) self.icepq = IceQuiverPostprocess(root_dir=self.root_dir, use_sge=self.sge_opts.use_sge, quit_if_not_done=False, ipq_opts=self.ipq_opts) self.add_log("IceQuiverPostprocess log: {f}.". format(f=self.icepq.log_fn), level=logging.INFO) self.icepq.run() self.add_log("IceQuiverPostprocess finished.", level=logging.INFO)
class Polish(IceFiles): """Polish isoforms clusters using Quiver.""" def __init__(self, root_dir, nfl_fa, bas_fofn, ccs_fofn, ice_opts, sge_opts, hq_isoforms_fa=None, hq_isoforms_fq=None, lq_isoforms_fa=None, lq_isoforms_fq=None, fasta_fofn=None): """ root_dir --- IceFiles.root_dir, usually data/clusterOutDir nfl_fa --- non-full-length reads in fasta, e.g., isoseq_nfl.fa bas_fofn --- e.g. input.fofn of bas|bax.h5 files ccs_fofn --- e.g. reads_of_insert.fofn of ccs files. hq_isoforms_fa|fq --- polished, hiqh quality consensus isoforms in fasta|q lq_isoforms_fa|fq --- polished, low quality consensus isoforms in fasta|q """ IceFiles.__init__(self, prog_name="IcePolish", root_dir=root_dir, bas_fofn=bas_fofn, ccs_fofn=ccs_fofn, fasta_fofn=fasta_fofn) self.nfl_fa = realpath(nfl_fa) self.hq_isoforms_fa = hq_isoforms_fa self.hq_isoforms_fq = hq_isoforms_fq self.lq_isoforms_fa = lq_isoforms_fa self.lq_isoforms_fq = lq_isoforms_fq self.ice_opts = ice_opts self.sge_opts = sge_opts self.icep = None # IceAllPartials. self.iceq = None # IceQuiver self.icepq = None # IcePostQuiver self._nfl_splitted_fas = None self._validate_inputs() def _validate_inputs(self): """ Validate input directories: root_dir, and files: nfl_fa, bas_fofn, ccs_fofn. """ self.add_log("Validating inputs.") errMsg = "" if not op.exists(self.root_dir): errMsg = "Root dir {d} is not an existing directory!".\ format(d=self.root_dir) if not op.exists(self.nfl_fa): errMsg = "Failed to find non-full-length reads {f}!".\ format(f=self.nfl_fa) if not op.exists(self.bas_fofn): errMsg = "Failed to find bas fofn {f}!".format(f=self.bas_fofn) if errMsg != "": self.add_log(errMsg, level=logging.ERROR) raise ValueError(errMsg) def get_sa_file(self): """Return saffix array of final_consensus_fa.""" ret = True if not op.exists(self.final_consensus_sa): ret = build_sa(self.final_consensus_fa, self.final_consensus_sa) if ret is True: self.add_log("Successfully created a suffix array for {f} at {sa}.". format(f=self.final_consensus_fa, sa=self.final_consensus_sa)) else: self.add_log("Failed to generate suffix array for {f}".format( f=self.final_consensus_fa), level=logging.WARNING) if op.exists(self.final_consensus_sa): return self.final_consensus_sa else: return None 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)