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, 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
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)