diff --git a/.gitignore b/.gitignore index 35e0cd8..db19e92 100644 --- a/.gitignore +++ b/.gitignore @@ -44,6 +44,8 @@ phylophlan/examples/tutorial* ## other internal runs phylophlan/examples/paper_examples phylophlan/examples/pcopri +## any other files inside examples +phylophlan/examples/*.* # settings files .vscode # temp files and folders diff --git a/phylophlan/phylophlan_metagenomic.py b/phylophlan/phylophlan_assign_sgbs.py similarity index 98% rename from phylophlan/phylophlan_metagenomic.py rename to phylophlan/phylophlan_assign_sgbs.py index b921fd6..5926905 100755 --- a/phylophlan/phylophlan_metagenomic.py +++ b/phylophlan/phylophlan_assign_sgbs.py @@ -8,8 +8,8 @@ 'Mattia Bolzan (mattia.bolzan@unitn.it), ' 'Paolo Manghi (paolo.manghi@unitn.it), ' 'Nicola Segata (nicola.segata@unitn.it)') -__version__ = '3.0.39' -__date__ = '28 September 2023' +__version__ = '3.0.40' +__date__ = '5 February 2024' import sys @@ -37,7 +37,7 @@ HOW_MANY = "8" #DOWNLOAD_URL = "https://www.dropbox.com/s/xdqm836d2w22npb/phylophlan_metagenomic.txt?dl=1" -DOWNLOAD_URL = "http://cmprod1.cibio.unitn.it/databases/PhyloPhlAn/phylophlan_metagenomic_new.txt" +DOWNLOAD_URL = "http://cmprod1.cibio.unitn.it/databases/PhyloPhlAn/phylophlan_SGB_databases.txt" DATABASE_FOLDER = 'phylophlan_databases/' @@ -64,7 +64,7 @@ def error(s, init_new_line=False, exit=False, exit_value=1): def read_params(): - p = ap.ArgumentParser(description=("The phylophlan_metagenomic.py script assign SGB and taxonomy to a given set of input genomes. " + p = ap.ArgumentParser(description=("The phylophlan_assign_sgbs.py script assigns the SGB and taxonomy to a given set of input genomes. " "Outputs can be of three types: (1) for each input genomes returns the list of the closest " "-n/--how_many SGBs sorted by average Mash distance; (2) for each input genomes returns the " "closest SGB, GGB, FGB, and reference genomes; (3) returns a all vs. all matrix with all the " @@ -72,7 +72,7 @@ def read_params(): formatter_class=ap.ArgumentDefaultsHelpFormatter) p.add_argument('-i', '--input', type=str, - help="Input folder containing the metagenomic bins to be indexed") + help="Input folder containing genomes and/or metagenome-assembled genomes (MAGs) to be indexed") p.add_argument('-o', '--output_prefix', type=str, default=None, help=("Prefix used for the output folders: indexed bins, distance estimations. If not specified, " "the input folder will be used")) @@ -104,8 +104,8 @@ def read_params(): help="Show citation") p.add_argument('--verbose', action='store_true', default=False, help="Prints more stuff") p.add_argument('-v', '--version', action='version', - version='phylophlan_metagenomic.py version {} ({})'.format(__version__, __date__), - help="Prints the current phylophlan_metagenomic.py version and exit") + version='phylophlan_assign_sgbs.py version {} ({})'.format(__version__, __date__), + help="Prints the current phylophlan_assign_sgbs.py version and exit") return p.parse_args() @@ -730,7 +730,7 @@ def group_assignment(output_prefix, db, groups_map, nproc=1, verbose=True): sgb_repr = row.strip().split('\t')[0] for sgb in row.strip().split('\t'): - sgb_2_group[f'SGB{sgb}'] = f'SGB{sgb_repr}_group' + sgb_2_group[sgb] = f'{sgb_repr}_group' return sgb_2_group @@ -889,7 +889,7 @@ def phylophlan_metagenomic(): args = read_params() if args.verbose: - info('phylophlan_metagenomic.py version {} ({})\n'.format(__version__, __date__)) + info('phylophlan_assign_sgbs.py version {} ({})\n'.format(__version__, __date__)) info('Command line: {}\n\n'.format(' '.join(sys.argv)), init_new_line=True) check_params(args, verbose=args.verbose) @@ -1107,7 +1107,7 @@ def phylophlan_metagenomic(): # group_assignment if sgb_id in sgb_2_group: - sgb_id=sgb_2_group[sgb_id] + sgb_id = sgb_2_group[sgb_id] f.write('\t'.join([binn, "{}_{}:{}:{}:{}".format(sgb_2_info[sgb_id.split('_')[0]][5], sgb_id, sgb_2_info[sgb_id.split('_')[0]][6],