def index_fasta(self):
"""index subreads in fasta_fofn, return"""
files = get_files_from_fofn(self.fasta_fofn)
msg = "Indexing {0} fasta files, please wait.".format(len(files))
self.add_log(msg)
d = MetaSubreadFastaReader(files)
self.add_log("Fasta files indexing done.")
return d
def index_fasta(self):
"""index subreads in fasta_fofn, return"""
files = get_files_from_fofn(self.fasta_fofn)
msg = "Indexing {0} fasta files, please wait.".format(len(files))
self.add_log(msg)
d = MetaSubreadFastaReader(files)
self.add_log("Fasta files indexing done.")
return d
def run(self):
"""Run quiver for ICE."""
# Create directories: root_dir/quivered and root_dir/log_dir/quivered
mkdir(self.quivered_dir)
mkdir(self.quivered_log_dir)
files = get_files_from_fofn(self.fasta_fofn)
msg = "Indexing {0} fasta files, please wait.".format(len(files))
self.add_log(msg)
d = MetaSubreadFastaReader(files)
self.add_log("Fasta files indexing done.")
self.add_log("Loading uc from {f}.".format(f=self.final_pickle_fn))
a = load(open(self.final_pickle_fn))
uc = a['uc']
refs = a['refs']
self.add_log("Loading partial uc from {f}.".
format(f=self.nfl_all_pickle_fn))
partial_uc = load(open(self.nfl_all_pickle_fn))['partial_uc']
partial_uc2 = defaultdict(lambda: [])
partial_uc2.update(partial_uc)
# Write report to quivered/cluster_report.FL_nonFL.csv
self.add_log("Writing a csv report of cluster -> FL/NonFL reads to {f}".
format(f=self.report_fn), level=logging.INFO)
self.write_report(uc=uc, partial_uc=partial_uc2,
report_fn=self.report_fn)
good = [x for x in uc] #[x for x in uc if len(uc[x]) > 1 or len(partial_uc2[x]) >= 10]
keys = sorted(good) # sort good keys (cluster ids)
start = 0
end = len(keys)
submitted = [] # submitted jobs
todo = [] # to-do jobs
self.submit_quiver_jobs(d=d, uc=uc, partial_uc=partial_uc2,
refs=refs, keys=keys, start=start, end=end,
submitted=submitted, todo=todo,
use_sge=self.sge_opts.use_sge,
max_sge_jobs=self.sge_opts.max_sge_jobs,
quiver_nproc=self.sge_opts.quiver_nproc)
with open(self.submitted_quiver_jobs_log, 'w') as f:
f.write("\n".join(str(x[0]) + '\t' + str(x[1]) for x in submitted))
self.close_log()
return 0
def validate_inputs(self):
"""Validate input fofns, and root_dir, log_dir, tmp_dir,
create quivered_dir and quivered_log_dir"""
self.add_log("Validating inputs.")
# Create directories: root_dir/quivered and root_dir/log_dir/quivered
try:
mkdir(self.quivered_dir)
mkdir(self.quivered_log_dir)
except OSError:
# Multiple ice_quiver_i jobs may run at the same time and try to
# mkdir, race condition may happen, so ignore OSError here.
pass
errMsg = ""
if not nfs_exists(self.log_dir) or not op.isdir(self.log_dir):
errMsg = "Log dir {l} is not an existing directory.".\
format(l=self.log_dir)
elif self.bas_fofn is None:
errMsg = "Please specify bas_fofn (e.g. input.fofn)."
elif not nfs_exists(self.bas_fofn):
errMsg = "bas_fofn {f} ".format(f=self.bas_fofn) + \
"which contains bas/bax.h5 files does not exist."
elif self.fasta_fofn is None:
errMsg = "Please make sure ice_make_fasta_fofn has " + \
"been called, and specify fasta_fofn."
elif not nfs_exists(self.fasta_fofn):
errMsg = "Input fasta_fofn {f} does not exists.".\
format(f=self.fasta_fofn)
fasta_files = get_files_from_fofn(self.fasta_fofn)
for fasta_file in fasta_files:
if not nfs_exists(fasta_file):
errMsg = "A file {f} in fasta_fofn does not exist.".\
format(f=fasta_file)
elif not nfs_exists(self.nfl_all_pickle_fn):
#"output/map_noFL/noFL.ALL.partial_uc.pickle"):
errMsg = "Pickle file {f} ".format(f=self.nfl_all_pickle_fn) + \
"which assigns all non-full-length reads to isoforms " + \
"does not exist. Please check 'ice_partial.py *' are " + \
"all done."
elif not nfs_exists(self.final_pickle_fn):
errMsg = "Pickle file {f} ".format(f=self.final_pickle_fn) + \
"which assigns full-length non-chimeric reads to " + \
"isoforms does not exist."
if errMsg != "":
self.add_log(errMsg, level=logging.ERROR)
raise IOError(errMsg)
def validate_inputs(self):
"""Validate input fofns, and root_dir, log_dir, tmp_dir,
create quivered_dir and quivered_log_dir"""
self.add_log("Validating inputs.")
# Create directories: root_dir/quivered and root_dir/log_dir/quivered
try:
mkdir(self.quivered_dir)
mkdir(self.quivered_log_dir)
except OSError:
# Multiple ice_quiver_i jobs may run at the same time and try to
# mkdir, race condition may happen, so ignore OSError here.
pass
errMsg = ""
if not nfs_exists(self.log_dir) or not op.isdir(self.log_dir):
errMsg = "Log dir {l} is not an existing directory.".\
format(l=self.log_dir)
elif self.bas_fofn is None:
errMsg = "Please specify bas_fofn (e.g. input.fofn)."
elif not nfs_exists(self.bas_fofn):
errMsg = "bas_fofn {f} ".format(f=self.bas_fofn) + \
"which contains bas/bax.h5 files does not exist."
elif self.fasta_fofn is None:
errMsg = "Please make sure ice_make_fasta_fofn has " + \
"been called, and specify fasta_fofn."
elif not nfs_exists(self.fasta_fofn):
errMsg = "Input fasta_fofn {f} does not exists.".\
format(f=self.fasta_fofn)
fasta_files = get_files_from_fofn(self.fasta_fofn)
for fasta_file in fasta_files:
if not nfs_exists(fasta_file):
errMsg = "A file {f} in fasta_fofn does not exist.".\
format(f=fasta_file)
elif not nfs_exists(self.nfl_all_pickle_fn):
#"output/map_noFL/noFL.ALL.partial_uc.pickle"):
errMsg = "Pickle file {f} ".format(f=self.nfl_all_pickle_fn) + \
"which assigns all non-full-length reads to isoforms " + \
"does not exist. Please check 'ice_partial.py *' are " + \
"all done."
elif not nfs_exists(self.final_pickle_fn):
errMsg = "Pickle file {f} ".format(f=self.final_pickle_fn) + \
"which assigns full-length non-chimeric reads to " + \
"isoforms does not exist."
if errMsg != "":
self.add_log(errMsg, level=logging.ERROR)
raise IOError(errMsg)
def run(self):
"""Run quiver for ICE."""
# Create directories: root_dir/quivered and root_dir/log_dir/quivered
mkdir(self.quivered_dir)
mkdir(self.quivered_log_dir)
files = get_files_from_fofn(self.fasta_fofn)
msg = "Indexing {0} fasta files, please wait.".format(len(files))
self.add_log(msg)
d = MetaSubreadFastaReader(files)
self.add_log("Fasta files indexing done.")
self.add_log("Loading uc from {f}.".format(f=self.final_pickle_fn))
a = load(open(self.final_pickle_fn))
uc = a['uc']
refs = a['refs']
self.add_log(
"Loading partial uc from {f}.".format(f=self.nfl_all_pickle_fn))
partial_uc = load(open(self.nfl_all_pickle_fn))['partial_uc']
partial_uc2 = defaultdict(lambda: [])
partial_uc2.update(partial_uc)
# Write report to quivered/cluster_report.FL_nonFL.csv
self.add_log(
"Writing a csv report of cluster -> FL/NonFL reads to {f}".format(
f=self.report_fn),
level=logging.INFO)
self.write_report(uc=uc,
partial_uc=partial_uc2,
report_fn=self.report_fn)
good = [
x for x in uc
] #[x for x in uc if len(uc[x]) > 1 or len(partial_uc2[x]) >= 10]
keys = sorted(good) # sort good keys (cluster ids)
start = 0
end = len(keys)
submitted = [] # submitted jobs
todo = [] # to-do jobs
self.submit_quiver_jobs(d=d,
uc=uc,
partial_uc=partial_uc2,
refs=refs,
keys=keys,
start=start,
end=end,
submitted=submitted,
todo=todo,
use_sge=self.sge_opts.use_sge,
max_sge_jobs=self.sge_opts.max_sge_jobs,
quiver_nproc=self.sge_opts.quiver_nproc)
with open(self.submitted_quiver_jobs_log, 'w') as f:
f.write("\n".join(str(x[0]) + '\t' + str(x[1]) for x in submitted))
self.close_log()
return 0
