def __init__(self,
prog_name,
root_dir,
bas_fofn=None,
ccs_fofn=None,
fasta_fofn=None,
no_log_f=False,
tmp_dir=None,
make_dirs=True):
"""
prog_name --- name of a sub-class
root_dir --- root directory of the whole project. There will be
sub-directories under it, including:
tmp/ --- 0/ c0, c1, ..., c9999
--- 1/ c10000, c10001, ..., c19999
...
each c? folder contains data for a cluster id=c?
script/
--- 0/ gcon_job_?.sh, gcon jobs in the first iteration
--- 1/ gcon_job_?.sh, gcon jobs in the second iteration
...
log/
--- ICE.log Log of the ICE algorithm
--- 0/ log for jobs in the first iteration
...
output/ output files go here.
bas_fofn --- input.fofn which contains movie.bas|bax.h5 files.
ccs_fofn --- a fofn contains movie.ccs.h5 files.
fasta_fofn --- a fofn contains movie.bax.h5.fasta files.
script/
no_log_f --- DON'T write log to a log file.
tmp_dir --- Write temporary files to tmp_dir (usually /scratch) for speed
"""
self.prog_name = str(prog_name)
self.root_dir = real_ppath(root_dir)
self._tmp_dir = real_ppath(tmp_dir)
self.bas_fofn = real_ppath(bas_fofn)
self.ccs_fofn = real_ppath(ccs_fofn)
self.fasta_fofn = real_ppath(fasta_fofn)
if make_dirs is True:
mkdir(self.root_dir)
mkdir(self.tmp_dir)
mkdir(self.log_dir)
mkdir(self.script_dir)
mkdir(self.out_dir)
self.no_log_f = no_log_f
if not no_log_f:
self.log_f = open(self.log_fn, 'w', 0)
self.add_log(msg="{p} initialized.".format(p=self.prog_name))
def run(self):
"""Run"""
logging.debug("root_dir: {d}.".format(d=self.root_dir))
logging.debug("nfl_fa: {f}.".format(f=self.nfl_fa))
logging.debug("Total number of chunks: N={N}.".format(N=self.N))
# Validate input files,
(num_reads, reads_per_split, nfl_dir, splitted_fas_todo) = \
self.validate_inputs()
logging.info("Total number of reads is {n}.".format(n=num_reads))
logging.info("Splitting nfl_fa into chunks each " +
"containing {n} reads.".format(n=reads_per_split))
splitted_fas_done = splitFasta(
input_fasta=real_ppath(self.nfl_fa),
reads_per_split=reads_per_split,
out_dir=nfl_dir,
out_prefix="input.split")
logging.info("Splitted files are: " + "\n".join(splitted_fas_done))
for fa in splitted_fas_todo:
if fa not in splitted_fas_done:
logging.info("touching {f}".format(f=fa))
touch(fa)
def __init__(self, prog_name, root_dir,
bas_fofn=None, ccs_fofn=None, fasta_fofn=None,
no_log_f=False, tmp_dir=None, make_dirs=True):
"""
prog_name --- name of a sub-class
root_dir --- root directory of the whole project. There will be
sub-directories under it, including:
tmp/ --- 0/ c0, c1, ..., c9999
--- 1/ c10000, c10001, ..., c19999
...
each c? folder contains data for a cluster id=c?
script/
--- 0/ gcon_job_?.sh, gcon jobs in the first iteration
--- 1/ gcon_job_?.sh, gcon jobs in the second iteration
...
log/
--- ICE.log Log of the ICE algorithm
--- 0/ log for jobs in the first iteration
...
output/ output files go here.
bas_fofn --- input.fofn which contains movie.bas|bax.h5 files.
ccs_fofn --- a fofn contains movie.ccs.h5 files.
fasta_fofn --- a fofn contains movie.bax.h5.fasta files.
script/
no_log_f --- DON'T write log to a log file.
tmp_dir --- Write temporary files to tmp_dir (usually /scratch) for speed
"""
self.prog_name = str(prog_name)
self.root_dir = real_ppath(root_dir)
self._tmp_dir = real_ppath(tmp_dir)
self.bas_fofn = real_ppath(bas_fofn)
self.ccs_fofn = real_ppath(ccs_fofn)
self.fasta_fofn = real_ppath(fasta_fofn)
if make_dirs is True:
mkdir(self.root_dir)
mkdir(self.tmp_dir)
mkdir(self.log_dir)
mkdir(self.script_dir)
mkdir(self.out_dir)
self.no_log_f = no_log_f
if not no_log_f:
self.log_f = open(self.log_fn, 'w', 0)
self.add_log(msg="{p} initialized.".format(p=self.prog_name))
def run(self):
"""Run"""
logging.debug("root_dir: {d}.".format(d=self.root_dir))
logging.debug("nfl_fa: {f}.".format(f=self.nfl_fa))
logging.debug("Total number of chunks: N={N}.".format(N=self.N))
# Validate input files,
(num_reads, reads_per_split, nfl_dir, splitted_fas_todo) = \
self.validate_inputs()
logging.info("Total number of reads is {n}.".format(n=num_reads))
logging.info("Splitting nfl_fa into chunks each " +
"containing {n} reads.".format(n=reads_per_split))
splitted_fas_done = splitFasta(input_fasta=real_ppath(self.nfl_fa),
reads_per_split=reads_per_split,
out_dir=nfl_dir,
out_prefix="input.split")
logging.info("Splitted files are: " + "\n".join(splitted_fas_done))
for fa in splitted_fas_todo:
if fa not in splitted_fas_done:
logging.info("touching {f}".format(f=fa))
touch(fa)