def print_version_and_exit(version): options_storage.version(version, mode="tru") sys.exit(0)
def main(): all_long_options = list(set(options_storage.long_options + dipspades_logic.DS_Args_List.long_options)) all_short_options = options_storage.short_options + dipspades_logic.DS_Args_List.short_options dipspades_logic_args = [] spades_py_args = ["--diploid"] try: options, not_options = getopt.gnu_getopt(sys.argv, all_short_options, all_long_options) except getopt.GetoptError: _, exc, _ = sys.exc_info() sys.stderr.write(str(exc) + "\n") options_storage.usage(spades_version, mode="dip") sys.stderr.flush() sys.exit(1) if not options: options_storage.usage(spades_version, mode="dip") sys.stderr.flush() sys.exit(1) output_dir = None spades_py_run_needed = False for opt, arg in options: # processing some special options if opt == '--test': output_dir = abspath("test_dipspades") spades_py_args = ["--diploid", "-1", os.path.join(spades_init.spades_home, "test_dataset/ecoli_1K_1.fq.gz"), "-2", os.path.join(spades_init.spades_home, "test_dataset/ecoli_1K_2.fq.gz"), "--only-assembler"] dipspades_logic_args = [] spades_py_run_needed = True break if opt == '-o': output_dir = abspath(expanduser(arg)) elif opt == '--careful' or opt == '--mismatch-correction': continue if opt == '-v' or opt == '--version': options_storage.version(spades_version, mode="dip") sys.exit(0) if opt == '-h' or opt == '--help': options_storage.usage(spades_version, mode="dip") sys.exit(0) elif opt == "--help-hidden": options_storage.usage(spades_version, show_hidden=True, mode="dip") sys.exit(0) # for all other options cur_opt_arg = [opt] if arg: cur_opt_arg.append(arg) if opt.startswith("--"): # long option if opt[2:] in options_storage.long_options or (opt[2:] + "=") in options_storage.long_options: spades_py_args += cur_opt_arg if opt[2:] in dipspades_logic.DS_Args_List.long_options or (opt[2:] + "=") in dipspades_logic.DS_Args_List.long_options: dipspades_logic_args += cur_opt_arg else: spades_py_run_needed = True else: dipspades_logic_args += cur_opt_arg else: # short option if opt != '-o': if opt[1:] in options_storage.short_options: spades_py_args += cur_opt_arg if opt[1:] in dipspades_logic.DS_Args_List.short_options: dipspades_logic_args += cur_opt_arg else: spades_py_run_needed = True else: dipspades_logic_args += cur_opt_arg if not output_dir: support.error("The output_dir is not set! It is a mandatory parameter (-o output_dir).", dipspades=True) spades_output_dir = os.path.join(output_dir, "spades") dipspades_output_dir = os.path.join(output_dir, "dipspades") if not os.path.isdir(output_dir): os.makedirs(output_dir) if not os.path.isdir(spades_output_dir): os.makedirs(spades_output_dir) if not os.path.isdir(dipspades_output_dir): os.makedirs(dipspades_output_dir) spades_result = "" if spades_py_run_needed: spades_py_args += ["-o", spades_output_dir] spades.main(spades_py_args) spades_result = os.path.join(spades_output_dir, "contigs.fasta") if not os.path.isfile(spades_result): support.error("Something went wrong and SPAdes did not generate haplocontigs. " "DipSPAdes cannot proceed without them, aborting.", dipspades=True) dipspades_logic_args += ["-o", dipspades_output_dir] if spades_result != "": dipspades_logic_args += ["--hap", spades_result] dipspades_logic.main(dipspades_logic_args, sys.argv, spades.spades_home, spades.bin_home)
def main(): all_long_options = list( set(options_storage.long_options + dipspades_logic.DS_Args_List.long_options)) all_short_options = options_storage.short_options + dipspades_logic.DS_Args_List.short_options dipspades_logic_args = [] spades_py_args = ["--diploid"] try: options, not_options = getopt.gnu_getopt(sys.argv, all_short_options, all_long_options) except getopt.GetoptError: _, exc, _ = sys.exc_info() sys.stderr.write(str(exc) + "\n") options_storage.usage(spades_version, mode="dip") sys.stderr.flush() sys.exit(1) if not options: options_storage.usage(spades_version, mode="dip") sys.stderr.flush() sys.exit(1) output_dir = None spades_py_run_needed = False for opt, arg in options: # processing some special options if opt == '--test': output_dir = abspath("test_dipspades") spades_py_args = [ "--diploid", "-1", os.path.join(spades_init.spades_home, "test_dataset/ecoli_1K_1.fq.gz"), "-2", os.path.join(spades_init.spades_home, "test_dataset/ecoli_1K_2.fq.gz"), "--only-assembler" ] dipspades_logic_args = [] spades_py_run_needed = True break if opt == '-o': output_dir = abspath(expanduser(arg)) elif opt == '--careful' or opt == '--mismatch-correction': continue if opt == '-v' or opt == '--version': options_storage.version(spades_version, mode="dip") sys.exit(0) if opt == '-h' or opt == '--help': options_storage.usage(spades_version, mode="dip") sys.exit(0) elif opt == "--help-hidden": options_storage.usage(spades_version, show_hidden=True, mode="dip") sys.exit(0) # for all other options cur_opt_arg = [opt] if arg: cur_opt_arg.append(arg) if opt.startswith("--"): # long option if opt[2:] in options_storage.long_options or ( opt[2:] + "=") in options_storage.long_options: spades_py_args += cur_opt_arg if opt[2:] in dipspades_logic.DS_Args_List.long_options or ( opt[2:] + "=") in dipspades_logic.DS_Args_List.long_options: dipspades_logic_args += cur_opt_arg else: spades_py_run_needed = True else: dipspades_logic_args += cur_opt_arg else: # short option if opt != '-o': if opt[1:] in options_storage.short_options: spades_py_args += cur_opt_arg if opt[1:] in dipspades_logic.DS_Args_List.short_options: dipspades_logic_args += cur_opt_arg else: spades_py_run_needed = True else: dipspades_logic_args += cur_opt_arg if not output_dir: support.error( "The output_dir is not set! It is a mandatory parameter (-o output_dir).", dipspades=True) spades_output_dir = os.path.join(output_dir, "spades") dipspades_output_dir = os.path.join(output_dir, "dipspades") if not os.path.isdir(output_dir): os.makedirs(output_dir) if not os.path.isdir(spades_output_dir): os.makedirs(spades_output_dir) if not os.path.isdir(dipspades_output_dir): os.makedirs(dipspades_output_dir) spades_result = "" if spades_py_run_needed: spades_py_args += ["-o", spades_output_dir] spades.main(spades_py_args) spades_result = os.path.join(spades_output_dir, "contigs.fasta") if not os.path.isfile(spades_result): support.error( "Something went wrong and SPAdes did not generate haplocontigs. " "DipSPAdes cannot proceed without them, aborting.", dipspades=True) dipspades_logic_args += ["-o", dipspades_output_dir] if spades_result != "": dipspades_logic_args += ["--hap", spades_result] dipspades_logic.main(dipspades_logic_args, sys.argv, spades.spades_home, spades.bin_home)
def print_version_and_exit(version): options_storage.version(version, mode="TruSPAdes") sys.exit(0)
def show_version(): options_storage.version(spades_version) sys.exit(0)