`PanACoTA.all_modules` package¶

`all` module¶

‘all’ is a module of PanACoTA, allowing to run the whole pipeline at once.

@author gem October 2020

PanACoTA.subcommands.all_modules.build_parser(parser)¶

Method to create a parser for command-line options

Parameters:

PanACoTA.subcommands.all_modules.check_args(parser, argv)¶

Check arguments given by user

Parameters:

Returns:

PanACoTA.subcommands.all_modules.get_align(dict_argv)¶: Check that arguments given for align step are compatible

PanACoTA.subcommands.all_modules.get_annotate(dict_argv)¶: Check that arguments given for annotate step are compatible

PanACoTA.subcommands.all_modules.get_corepers(dict_argv)¶: Check that arguments given for corepers step are compatible

PanACoTA.subcommands.all_modules.get_pangenome(dict_argv)¶: Check that arguments given for pangenome step are compatible

PanACoTA.subcommands.all_modules.get_prepare(dict_argv)¶: Check that arguments given for prepare step are compatible

PanACoTA.subcommands.all_modules.get_tree(dict_argv)¶: Check that arguments given for tree step are compatible

PanACoTA.subcommands.all_modules.main(cmd, args_all, args_prepare, args_annot, args_pan, args_corepers, args_align, args_tree)¶

Call all modules, one by one, using output of one as input for the next one

Parameters:

cmdstr: command line used to launch the program
args_alltuple: arguments common to all modules: output directory (str), threads (int), verbose (int), quiet (bool)
args_preparetuple: arguments for prepare module (see subcommands.prepare.py): NCBI_species_taxid (int), NCBI_species_name (str), NCBI_species_taxid (int), NCBI_taxid (int), NCBI_strains (str), levels (str), NCBI_section (str), tmp_dir (str), norefseq (bool), db_dir (str), only_mash (bool), info_file (str), l90 (int), nbcont (int), cutn (int), min_dist (float), max_dist (float)
args_annottuple: arguments for annotate module (see subcommands/annotate.py): name (str), qc_only (bool), date (str), prodigal_only (bool), small (bool)
args_pantuple: arguments for pangenome module (see subcommands/pangenome.py): min_id (float), clust_mode (int), spe_dir (str), outfile (str)
args_coreperstuple: arguments for corepers module (see subcommands.corepers.py): tol (float), mixed (bool), multi (bool), floor (bool)
args_aligntuple: arguments for align module (see subcommands.align.py): prot_ali (bool)
args_treetuple: arguments for tree module (see subcommands.tree.py): soft (str), model (str), boot (bool), write_boot (bool), memory (str), fast (bool)

PanACoTA.subcommands.all_modules.main_from_parse(args)¶

Call main function from the arguments given by parser

verbosity:

Parameters:

args_alltuple: arguments common to all modules: output directory (str), threads (int), verbose (int), quiet (bool)
args_preparetuple: arguments for prepare module (see subcommands.prepare.py): NCBI_species (str), NCBI_species_taxid (int), NCBI_taxid (int), strains (str), levels (str), NCBI_section (str), tmp_dir (str), norefseq (bool), db_dir (str), only_mash (bool), info_file (str), l90 (int), nbcont (int), cutn (int), min_dist (float), max_dist (float)
args_annottuple: arguments for annotate module (see subcommands/annotate.py): name (str), qc_only (bool), date (str), prodigal_only (bool), small (bool)
args_pantuple: arguments for pangenome module (see subcommands/pangenome.py): min_id (float), clust_mode (int), spe_dir (str), outfile (str)
args_coreperstuple: arguments for corepers module (see subcommands.corepers.py): tol (float), mixed (bool), multi (bool), floor (bool)
args_aligntuple: arguments for align module (see subcommands.align.py): prot_ali (bool)
args_treetuple: arguments for tree module (see subcommands.tree.py): soft (str), model (str), boot (bool), write_boot (bool), memory (str), fast (bool)

PanACoTA.subcommands.all_modules.parse(parser, argu)¶

parse arguments given to parser

Parameters:

Returns: