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) ]