def run(self):
"""Run"""
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)
iceq.validate_inputs()
iceq.run()
icepq = IceQuiverPostprocess(root_dir=self.root_dir,
use_sge=self.sge_opts.use_sge,
quit_if_not_done=False,
ipq_opts=self.ipq_opts)
icepq.run()
return 0
def run(self):
"""Run"""
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)
iceq.validate_inputs()
iceq.run()
icepq = IceQuiverPostprocess(root_dir=self.root_dir,
use_sge=self.sge_opts.use_sge,
quit_if_not_done=False,
ipq_opts=self.ipq_opts)
icepq.run()
return 0
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()