def get_command(self, cfg):
return [commands_parser.Command(STAGE=self.STAGE_NAME,
path="true",
args=[],
short_name=self.short_name + "_start")] + \
[x for stage in self.stages for x in stage.get_command(self.cfg)] + \
[commands_parser.Command(STAGE=self.STAGE_NAME,
path="true",
args=[],
short_name=self.short_name + "_finish")]
def get_command(self, cfg):
return [commands_parser.Command(STAGE=self.STAGE_NAME,
path="true",
args=[],
short_name=self.short_name + "_start")] + \
[x for stage in self.stages for x in stage.get_command(cfg)] + \
[commands_parser.Command(STAGE=self.STAGE_NAME,
path="true",
args=[],
short_name=self.short_name + "_finish",
del_after=[os.path.relpath(self.tmp_dir, options_storage.args.output_dir)])]
def get_command(self, cfg):
dst_configs = os.path.join(cfg.output_dir, "configs")
if cfg.iontorrent:
cfg_file_name = os.path.join(dst_configs, "ionhammer.cfg")
else:
cfg_file_name = os.path.join(dst_configs, "config.info")
if cfg.iontorrent:
binary_name = "spades-ionhammer"
else:
binary_name = "spades-hammer"
command = [
commands_parser.Command(
STAGE="Read error correction",
path=os.path.join(self.bin_home, binary_name),
args=[os.path.abspath(cfg_file_name)],
config_dir=os.path.relpath(cfg.output_dir,
options_storage.args.output_dir),
short_name=self.short_name,
del_after=[cfg.tmp_dir],
output_files=[
self.output_files["corrected_dataset_yaml_filename"]
])
]
return command
def get_command(self, cfg):
args = [
os.path.join(self.python_modules_home, "spades_pipeline",
"scripts", "check_test_script.py")
]
if options_storage.args.truseq_mode:
args += [
"--mode", "truseq", "--truseq_long_reads_file",
self.output_files["truseq_long_reads_file"]
]
elif options_storage.args.rna:
args += [
"--mode", "rna", "--result_transcripts_filename",
self.output_files["result_transcripts_filename"]
]
else:
if options_storage.args.plasmid:
args += ["--mode", "plasmid"]
else:
args += ["--mode", "common"]
args += [
"--result_contigs_filename",
self.output_files["result_contigs_filename"],
"--result_scaffolds_filename",
self.output_files["result_scaffolds_filename"]
]
return [
commands_parser.Command(STAGE=self.STAGE_NAME,
path=sys.executable,
args=args,
short_name=self.short_name)
]
def get_command(self, cfg):
args = [
os.path.join(self.python_modules_home, "spades_pipeline",
"scripts", "correction_iteration_script.py"),
"--corrected", self.corrected, "--assembled", self.assembled,
"--assembly_type", self.assembly_type, "--output_dir",
cfg["common"].output_dir, "--bin_home", self.bin_home
]
return [
commands_parser.Command(
STAGE=self.STAGE_NAME,
path=sys.executable,
args=args,
config_dir=os.path.relpath(self.cfg.output_dir,
options_storage.args.output_dir),
short_name=self.short_name,
del_after=[
os.path.join(
os.path.relpath(self.cfg.output_dir,
options_storage.args.output_dir),
"tmp"),
os.path.relpath(self.cfg.tmp_dir,
options_storage.args.output_dir)
])
]
def get_command(self, cfg):
self.cfg = cfg
self.set_output_files()
args = [
os.path.join(self.python_modules_home, "spades_pipeline",
"scripts", "copy_files.py")
]
for outputfile in self.output:
if outputfile.need_to_copy(outputfile, self.latest, self.cfg):
filename = os.path.join(self.latest, outputfile.tmp_file)
args.append(filename)
args.append(outputfile.output_file)
bin_reads_dir = os.path.join(self.cfg.output_dir, ".bin_reads")
command = [
commands_parser.Command(
STAGE=self.STAGE_NAME,
path=sys.executable,
args=args,
short_name=self.short_name,
del_after=[
os.path.relpath(bin_reads_dir,
options_storage.args.output_dir),
os.path.relpath(self.cfg.tmp_dir,
options_storage.args.output_dir)
])
]
return command
def get_command(self, cfg):
return [
commands_parser.Command(STAGE=self.STAGE_NAME,
path="true",
args=[],
short_name=self.short_name,
del_after=self.tmp_files)
]
def get_command(self, cfg):
args = [os.path.join(self.python_modules_home, "spades_pipeline", "scripts", "breaking_scaffolds_script.py"),
"--result_scaffolds_filename", self.output_files["result_scaffolds_filename"],
"--misc_dir", self.output_files["misc_dir"],
"--threshold_for_breaking_scaffolds", str(options_storage.THRESHOLD_FOR_BREAKING_SCAFFOLDS)]
return [commands_parser.Command(STAGE=self.STAGE_NAME,
path=sys.executable,
args=args,
short_name=self.short_name)]
def get_command(self, cfg):
del_after = []
if not cfg["common"].developer_mode:
del_after.append(self.tmp_configs_dir)
return [
commands_parser.Command(STAGE=self.STAGE_NAME,
path="true",
args=[],
short_name=self.short_name,
del_after=del_after)
]
def get_command(self, cfg):
data_dir = os.path.join(cfg.output_dir, "K%d" % self.K)
dst_configs = os.path.join(data_dir, "configs")
cfg_fn = os.path.join(dst_configs, "config.info")
args = [cfg_fn]
add_configs(args, dst_configs)
command = [commands_parser.Command(
STAGE="K%d" % self.K,
path=os.path.join(self.bin_home, "spades-core"),
args=args,
config_dir=os.path.relpath(data_dir, options_storage.args.output_dir),
short_name=self.short_name)]
return command
def get_command(self, cfg):
del_after = []
if not cfg["common"].developer_mode:
del_after.append(
os.path.relpath(self.tmp_configs_dir,
options_storage.args.output_dir))
return [
commands_parser.Command(STAGE=self.STAGE_NAME,
path="true",
args=[],
short_name=self.short_name,
del_after=del_after)
]
def get_command(self, cfg):
command = [
commands_parser.Command(
STAGE=self.STAGE_NAME,
path=sys.executable,
args=[
os.path.join(self.python_modules_home, "spades_pipeline",
"scripts", "preprocess_interlaced_reads.py"),
"--args_filename",
os.path.join(self.tmp_dir, "interlaced"), "--dst", self.dst
],
short_name=self.short_name)
]
return command
def get_command(self, cfg):
self.cfg = cfg
args = [
os.path.join(self.python_modules_home, "spades_pipeline",
"scripts", "plasmid_glue.py")
]
args.append(self.latest)
command = [
commands_parser.Command(
STAGE=self.STAGE_NAME,
path=sys.executable,
args=args,
short_name=self.short_name,
)
]
return command
def get_command(self, cfg):
command = [
commands_parser.Command(
STAGE=self.STAGE_NAME,
path=sys.executable,
args=[
os.path.join(self.python_modules_home, "spades_pipeline",
"scripts", "preprocess_nxmate_reads.py"),
"--args_filename",
os.path.join(self.tmp_dir,
"nxmate"), "--dst", self.dst, "--threads",
str(options_storage.args.threads)
],
short_name=self.short_name)
]
return command
def get_command(self, cfg):
command = [
commands_parser.Command(
STAGE=self.STAGE_NAME,
path=sys.executable,
args=[
os.path.join(self.python_modules_home, "spades_pipeline",
"scripts", "preprocess_contigs.py"),
"--args_filename",
os.path.join(self.tmp_dir, "contigs"), "--dst", self.dst,
"--threshold_for_breaking_additional_contigs",
str(options_storage.
THRESHOLD_FOR_BREAKING_ADDITIONAL_CONTIGS)
],
short_name=self.short_name)
]
return command
def get_command(self, cfg):
K = options_storage.SCC_K
data_dir = os.path.join(cfg.output_dir, "SCC", "K%d" % K)
dst_configs = os.path.join(data_dir, "configs")
cfg_file_name = os.path.join(dst_configs, "config.info")
args = [cfg_file_name]
add_configs(args, dst_configs)
command = [
commands_parser.Command(
STAGE="SCC",
path=os.path.join(self.bin_home,
"spades-truseq-scfcorrection"),
args=args,
config_dir=os.path.relpath(data_dir,
options_storage.args.output_dir),
short_name=self.short_name)
]
return command
def get_command(self, cfg):
args = [
os.path.join(self.python_modules_home, "spades_pipeline",
"scripts", "compress_all.py"), "--input_file",
self.output_files["corrected_dataset_yaml_filename"],
"--ext_python_modules_home", self.ext_python_modules_home,
"--max_threads",
str(cfg.max_threads), "--output_dir", cfg.output_dir
]
if cfg.not_used_dataset_yaml_filename != "":
args += [
"--not_used_yaml_file", cfg.not_used_dataset_yaml_filename
]
if cfg.gzip_output:
args.append("--gzip_output")
command = [
commands_parser.Command(STAGE="corrected reads compression",
path=sys.executable,
args=args,
short_name=self.short_name)
]
return command
def get_command(self, cfg):
# args: result_scaffolds_filename, assembled_scaffolds_filename, bin_home, ext_python_modules_home, output_dir, truseq_long_reads_file_base, dataset_yaml_file
args = [
os.path.join(self.python_modules_home, "spades_pipeline",
"scripts", "postprocessing_script.py"),
"--result_scaffolds_filename",
self.output_files["result_scaffolds_filename"],
"--assembled_scaffolds_filename",
self.output_files["assembled_scaffolds_filename"], "--bin_home",
self.bin_home, "--ext_python_modules_home",
self.ext_python_modules_home, "--output_dir",
cfg["common"].output_dir, "--truseq_long_reads_file_base",
self.output_files["truseq_long_reads_file_base"],
"--dataset_yaml_file", options_storage.args.dataset_yaml_filename,
"--threads",
str(options_storage.args.threads)
]
return [
commands_parser.Command(STAGE=self.STAGE_NAME,
path=sys.executable,
args=args,
short_name=self.short_name)
]
