API Reference

• panorama package
  • Subpackages
    • panorama.alignment package
      • Submodules
      • panorama.alignment.align module
      • panorama.alignment.cluster module
      • panorama.alignment.utils module
      • Module contents
    • panorama.annotate package
      • Submodules
      • panorama.annotate.annotate module
      • panorama.annotate.hmm_search module
      • Module contents
    • panorama.compare package
      • Submodules
      • panorama.compare.context module
      • panorama.compare.spots module
      • panorama.compare.systems module
      • panorama.compare.utils module
      • Module contents
    • panorama.format package
      • Submodules
      • panorama.format.read_binaries module
      • panorama.format.write_binaries module
      • panorama.format.write_flat module
      • panorama.format.write_proksee module
      • Module contents
    • panorama.info package
      • Submodules
      • panorama.info.info module
      • Module contents
    • panorama.systems package
      • Submodules
      • panorama.systems.detection module
      • panorama.systems.dictionary_validation_utils module
      • panorama.systems.models module
      • panorama.systems.parameter_validation_utils module
      • panorama.systems.system module
      • panorama.systems.systems_association module
      • panorama.systems.systems_partitions module
      • panorama.systems.systems_projection module
      • panorama.systems.utils module
      • panorama.systems.write_systems module
      • Module contents
    • panorama.utility package
      • Subpackages
      • Submodules
      • panorama.utility.genInput module
      • panorama.utility.utility module
      • Module contents
    • panorama.workflow package
      • Submodules
      • panorama.workflow.pansystems module
      • Module contents
  • Submodules
  • panorama.geneFamily module
    • Akin
      • Akin.ID
      • Akin.reference
      • Akin._families
      • Akin.__getitem__()
      • Akin.__init__()
      • Akin.__setitem__()
      • Akin.add()
      • Akin.get()
    • GeneFamily
      • GeneFamily.name
      • GeneFamily._hmm
      • GeneFamily.profile
      • GeneFamily.optimized_profile
      • GeneFamily._units_getter
      • GeneFamily._systems_getter
      • GeneFamily._akin
      • GeneFamily.HMM
      • GeneFamily.__eq__()
      • GeneFamily.__hash__()
      • GeneFamily.__init__()
      • GeneFamily.__ne__()
      • GeneFamily.__repr__()
      • GeneFamily._getattr_from_ppanggolin()
      • GeneFamily.akin
      • GeneFamily.is_multigenic()
      • GeneFamily.is_multigenic_in_org()
      • GeneFamily.module
      • GeneFamily.recast()
  • panorama.main module
  • panorama.pangenomes module
    • Pangenome
      • Pangenome.__init__()
      • Pangenome._create_gene_family()
      • Pangenome.add_file()
      • Pangenome.add_gene_family()
      • Pangenome.add_spot()
      • Pangenome.add_system()
      • Pangenome.gene_families
      • Pangenome.get_gene_family()
      • Pangenome.get_system()
      • Pangenome.get_system_by_source()
      • Pangenome.number_of_systems()
      • Pangenome.systems
      • Pangenome.systems_sources
      • Pangenome.systems_sources_to_metadata_source()
    • Pangenomes
      • Pangenomes.__init__()
      • Pangenomes.__iter__()
      • Pangenomes.__len__()
      • Pangenomes.add()
      • Pangenomes.add_cluster()
      • Pangenomes.add_cluster_systems()
      • Pangenomes.add_conserved_spots()
      • Pangenomes.cluster_systems
      • Pangenomes.conserved_spots
      • Pangenomes.get()
      • Pangenomes.get_cluster_systems()
      • Pangenomes.get_conserved_spots()
      • Pangenomes.get_family()
      • Pangenomes.items()
      • Pangenomes.mk_families_to_pangenome()
      • Pangenomes.number_of_cluster_systems
      • Pangenomes.number_of_conserved_spots
      • Pangenomes.read_clustering()
      • Pangenomes.to_list()
      • Pangenomes.to_set()
  • panorama.region module
    • ConservedSpots
      • ConservedSpots.__init__()
      • ConservedSpots.add()
      • ConservedSpots.get()
      • ConservedSpots.pangenomes()
      • ConservedSpots.spots
    • GeneContext
      • GeneContext.__init__()
      • GeneContext.summarize()
    • Module
      • Module.__init__()
      • Module.add_unit()
      • Module.gene_families
      • Module.get_unit()
      • Module.number_of_organisms
      • Module.organisms
      • Module.systems
      • Module.units
    • Region
      • Region.__init__()
    • Spot
      • Spot.__init__()
      • Spot.conserved
      • Spot.number_of_organisms
      • Spot.organisms
  • panorama.utils module
    • RawTextArgumentDefaultsHelpFormatter
    • add_common_arguments()
    • check_log()
    • check_tsv_sanity()
    • init_lock()
    • is_empty()
    • is_true_value()
    • mkdir()
    • pop_specific_action_grp()
    • set_verbosity_level()
  • Module contents
• Indices and tables