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_{0:03d}.fasta.partial_uc.pickle
splitted_pickles = [icef.nfl_pickle_i(i) for i in range(0, N)]
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, i, ccs_fofn, blasr_nproc, tmp_dir):
"""
Check inputs, write $ICE_PARTIAL_PY i command to script_file
and return (input_fasta, ref_fasta, 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.fasta
ref_fasta = icef.final_consensus_fa
ref_dazz = icef.final_dazz_db
# root_dir/output/map_noFL/input.split_{0:03d}.fasta
input_fasta = icef.nfl_fa_i(i)
# $input_fasta.partial_uc.pickle
out_pickle = icef.nfl_pickle_i(i)
# $input_fasta.partial_uc.pickle.DONE
done_file = icef.nfl_done_i(i)
# $input_fasta.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_PY split 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.")
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,
tmp_dir=tmp_dir)
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, out_pickle, done_file)
def _validate_inputs(self, root_dir, i, ccs_fofn, blasr_nproc, tmp_dir):
"""
Check inputs, write $ICE_PARTIAL_PY i command to script_file
and return (input_fasta, ref_fasta, 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.fasta
ref_fasta = icef.final_consensus_fa
ref_dazz = icef.final_dazz_db
# root_dir/output/map_noFL/input.split_{0:03d}.fasta
input_fasta = icef.nfl_fa_i(i)
# $input_fasta.partial_uc.pickle
out_pickle = icef.nfl_pickle_i(i)
# $input_fasta.partial_uc.pickle.DONE
done_file = icef.nfl_done_i(i)
# $input_fasta.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_PY split 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.")
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,
tmp_dir=tmp_dir)
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, out_pickle, done_file)
def _validate_inputs(self, root_dir, i, ccs_fofn, blasr_nproc, tmp_dir,
ref_fasta=None):
"""
Check inputs, write $ICE_PARTIAL_PY i command to script_file
and return (input_fasta, ref_fasta, 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.fasta
ref_fasta = icef.final_consensus_fa
ref_dazz = icef.final_dazz_db
# root_dir/output/map_noFL/input.split_{0:03d}.fasta
input_fasta = icef.nfl_fa_i(i)
# $input_fasta.partial_uc.pickle
out_pickle = icef.nfl_pickle_i(i)
# $input_fasta.partial_uc.pickle.DONE
done_file = icef.nfl_done_i(i)
# $input_fasta.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_PY split first.")
elif not nfs_exists(ref_fasta):
# ref_fasta --- root_dir/output/final.consensus.fasta
# ref_dazz --- root_dir/output/final.consensus.dazz.fasta.db
# ref_fasta and ref_dazz must exist if ICE has run successfully in
# root_dir. If either one does not exist, it means ICE has not
# successfully run in root_dir. Then we have to throw an error message
# requring users to copy the root_dir/output directory manually,
# rather than providing an option to overwrite ref_fasta and build
# ref_dazz, because a race condition can happen when multiple
# IcePartialI tasks start to run at the same time, which can corrupt
# fasta and dazz db files and lead to unexpected runtime errors.
errMsg = ("The unpolished consensus isoforms fasta file " +
"{f} does not exist. ".format(f=ref_fasta) +
"Please make sure ICE is successfully done in root_dir, " +
"or copy ICE output directory (e.g., cluster_out/output) " +
"to {dst}".format(dst=op.dirname(ref_fasta)))
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.")
if len(errMsg) != 0:
raise IOError(errMsg)
# Save cmd to script_file.
cmd = self._cmd_str(root_dir=root_dir, i=[i],
ccs_fofn=ccs_fofn,
blasr_nproc=blasr_nproc,
tmp_dir=tmp_dir)
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, out_pickle, done_file)
