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 ref_dazz = icef.final_dazz_db #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(ref_dazz): errMsg = ("The dazz db " + "{f} does not exist. ".format(f=ref_dazz) + "Please make sure it is already built.") # 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, ref_dazz, out_pickle, done_file)
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)