def run(self):
"""Run"""
iceq = IceQuiver(root_dir=self.root_dir, bas_fofn=None,
fasta_fofn=None, sge_opts=None,
prog_name="ice_quiver_merge")
iceq.add_log(self.cmd_str())
iceq.add_log("root_dir: {d}.".format(d=self.root_dir))
iceq.add_log("Total number of chunks: N = {N}.".format(N=self.N))
src = [iceq.submitted_quiver_jobs_log_of_chunk_i(i=i, num_chunks=self.N)
for i in range(0, self.N)]
for f in src:
if not nfs_exists(f):
raise IOError("Log {f} ".format(f=f) +
"of submitted quiver jobs does not exist.")
dst = iceq.submitted_quiver_jobs_log
iceq.add_log("Collecting submitted quiver jobs from:\n{src}\nto {dst}.".
format(src="\n".join(src), dst=dst))
cat_files(src=src, dst=dst)
iceq.close_log()
def run(self):
"""Run"""
iceq = IceQuiver(root_dir=self.root_dir, bas_fofn=None,
fasta_fofn=None, sge_opts=None,
prog_name="ice_quiver_merge")
iceq.add_log(self.cmd_str())
iceq.add_log("root_dir: {d}.".format(d=self.root_dir))
iceq.add_log("Total number of chunks: N = {N}.".format(N=self.N))
src = [iceq.submitted_quiver_jobs_log_of_chunk_i(i=i, num_chunks=self.N)
for i in range(0, self.N)]
for f in src:
if not nfs_exists(f):
raise IOError("Log {f} ".format(f=f) +
"of submitted quiver jobs does not exist.")
dst = iceq.submitted_quiver_jobs_log
iceq.add_log("Collecting submitted quiver jobs from:\n{src}\nto {dst}.".
format(src="\n".join(src), dst=dst))
cat_files(src=src, dst=dst)
iceq.close_log()
def run(self):
"""Run"""
for chunk in self.i:
iceq = IceQuiver(root_dir=self.root_dir,
bas_fofn=self.bas_fofn,
fasta_fofn=self.fasta_fofn,
sge_opts=self.sge_opts,
tmp_dir=self.tmp_dir,
prog_name="ice_quiver_{i}of{N}".format(i=chunk,
N=self.N))
cmd_str = self.cmd_str()
iceq.add_log(cmd_str)
iceq.add_log("root_dir: {d}.".format(d=self.root_dir))
iceq.add_log("Total number of chunks: N = {N}.".format(N=self.N))
iceq.add_log("Index of chunks: i = {i}.".format(i=chunk))
iceq.validate_inputs()
iceq.process_chunk_i(i=chunk, num_chunks=self.N)
iceq.close_log()
def run(self):
"""Run"""
for chunk in self.i:
iceq = IceQuiver(root_dir=self.root_dir,
bas_fofn=self.bas_fofn,
fasta_fofn=self.fasta_fofn,
sge_opts=self.sge_opts,
tmp_dir=self.tmp_dir,
prog_name="ice_quiver_{i}of{N}".
format(i=chunk, N=self.N))
cmd_str = self.cmd_str()
iceq.add_log(cmd_str)
iceq.add_log("root_dir: {d}.".format(d=self.root_dir))
iceq.add_log("Total number of chunks: N = {N}.".format(N=self.N))
iceq.add_log("Index of chunks: i = {i}.".format(i=chunk))
iceq.validate_inputs()
iceq.process_chunk_i(i=chunk, num_chunks=self.N)
iceq.close_log()