def _validate_inputs(self, root_dir, N): """ Check inputs, return (splitted_pickles, out_pickle) """ icef = IceFiles(prog_name="ice_partial_merge", root_dir=root_dir, no_log_f=False) # root_dir/output/map_noFL/input.split_{0:02d}.fa.partial_uc.pickle splitted_pickles = [icef.nfl_pickle_i(i) for i in range(0, N)] # root_dir/output/map_noFL/input.split_{0:02d}.fa.partial_uc.pickle.DONE dones = [icef.nfl_done_i(i) for i in range(0, N)] # Check if inputs exist. errMsg = "" for done in dones: if not nfs_exists(done): errMsg = "DONE file {f} does not exist.".format(f=done) for pickle in splitted_pickles: if not nfs_exists(pickle): errMsg = "Pickle file {f} does not exist.".format(f=pickle) if len(errMsg) != 0: raise ValueError(errMsg) # root_dir/output/map_noFL/nfl.all.partial_uc.pickle out_pickle = icef.nfl_all_pickle_fn return (splitted_pickles, out_pickle)
def _validate_inputs(self, root_dir, nfl_fa, N): """ Check inputs, return (num_reads, number_reads_per_chunk, nfl_dir, [i-th_chunk_nfl_fa for i in [0...N-1]]) """ icef = IceFiles(prog_name="ice_partial_split", root_dir=root_dir, no_log_f=False) nfl_dir = icef.nfl_dir # root_dir/output/map_noFL/input.split_{0:02d}.fa splitted_nfl_fas = [icef.nfl_fa_i(i) for i in range(0, N)] mkdir(icef.nfl_dir) # Check if inputs exist. errMsg = "" if not nfs_exists(nfl_fa): errMsg = ("The input non-full-length reads fasta file " + "{f} does not exists. ".format(f=nfl_fa)) if len(errMsg) != 0: raise ValueError(errMsg) num_reads = num_reads_in_fasta(nfl_fa) reads_per_split = int(max(1, ceil(num_reads / N))) return (num_reads, reads_per_split, nfl_dir, splitted_nfl_fas)
def _validate_inputs(self, root_dir, i, ccs_fofn, blasr_nproc): """ Check inputs, write ice_partial.py i command to script_file and return (input_fasta, ref_fasta, sa_file, out_pickle, done_file) for the i-th chunk of nfl reads. """ icef = IceFiles(prog_name="ice_partial_{i}".format(i=i), root_dir=root_dir, no_log_f=False) # root_dir/output/final.consensus.fa ref_fasta = icef.final_consensus_fa sa_file = icef.final_consensus_sa # root_dir/output/map_noFL/input.split_{0:02d}.fa input_fasta = icef.nfl_fa_i(i) # root_dir/output/map_noFL/input.split_{0:02d}.fa.partial_uc.pickle out_pickle = icef.nfl_pickle_i(i) # root_dir/output/map_noFL/input.split_{0:02d}.fa.partial_uc.pickle.DONE done_file = icef.nfl_done_i(i) # root_dir/scripts/input.split_{0:02d}.fa.partial_uc.sh script_file = icef.nfl_script_i(i) # Check if inputs exist. errMsg = "" if not nfs_exists(input_fasta): errMsg = ("The {i}-th splitted non-full-length reads ".format(i=i) + "fasta file {f} does not exist. ".format(f=input_fasta) + "Please run ice_partial_split.py first.") elif not nfs_exists(ref_fasta): errMsg = ("The unpolished consensus isoforms fasta file " + "{f} does not exist. ".format(f=ref_fasta) + "Please make sure ICE is successfully done.") elif not nfs_exists(sa_file): errMsg = ("The suffix array of unpolished consensus isoforms " + "(i.e., final_consensus_sa) {f} does not exist.") if len(errMsg) != 0: raise ValueError(errMsg) # Save cmd to script_file. cmd = self._cmd_str(root_dir=root_dir, i=i, ccs_fofn=ccs_fofn, blasr_nproc=blasr_nproc) with open(script_file, 'w') as writer: writer.write(cmd + "\n") icef.add_log("Writing CMD to: {script_file}". format(script_file=script_file)) icef.close_log() return (input_fasta, ref_fasta, sa_file, out_pickle, done_file)