capalyzer.packet_builder package

Subpackages

• capalyzer.packet_builder.sub_factories package
  • Submodules
  • capalyzer.packet_builder.sub_factories.amr_factory module
  • capalyzer.packet_builder.sub_factories.ave_genome_size_factory module
  • capalyzer.packet_builder.sub_factories.constants module
  • capalyzer.packet_builder.sub_factories.hmp_comparison_factory module
  • capalyzer.packet_builder.sub_factories.macrobes module
  • capalyzer.packet_builder.sub_factories.microbe_directory module
  • capalyzer.packet_builder.sub_factories.pathway_factory module
  • capalyzer.packet_builder.sub_factories.read_proportions module
  • capalyzer.packet_builder.sub_factories.subfactory module
  • capalyzer.packet_builder.sub_factories.taxonomy_factory module
  • capalyzer.packet_builder.sub_factories.toxonomy_long_form module
  • capalyzer.packet_builder.sub_factories.utils module
  • Module contents

Submodules

capalyzer.packet_builder.api module

capalyzer.packet_builder.api.make_all_tables(dirname, tables, overwrite=False)

Make a bunch of tables.

capalyzer.packet_builder.api.make_long_taxa(dirname, tables, overwrite=False)

Make a long format taxa table.

capalyzer.packet_builder.api.write_csv(df_func, fname, overwrite=False, **kwargs)

Build a dataframe and write a csv.

capalyzer.packet_builder.cli module

capalyzer.packet_builder.summary_table_factory module

class capalyzer.packet_builder.summary_table_factory.SummaryTableFactory(dirname, metadata_hooks=[])

Bases: object

A class that creates useful data tables from the MetaSUB CAP

get_metadata()

get_results(module=None, result=None)

Return [(<sample-name>, <file-type>, <file-name>)] for rtype.

capalyzer.packet_builder.utils module

capalyzer.packet_builder.utils.parse_key_val_file(filename, skip=0, skipchar='#', sep='\t', kind=<class 'float'>, key_column=0, val_column=1)

capalyzer.packet_builder.utils.readJSON(jsonf)

capalyzer.packet_builder.utils.tokenize(file_name, skip=0, sep='\t', skipchar='#')

Module contents