Integron_finder API Reference

• annotation
  • add_feature()
  • func_annot()
• attc
  • find_attc_max()
  • search_attc()
• config
  • Config
    • Config.__init__()
    • Config.__weakref__
    • Config.default_topology
    • Config.func_annot_path
    • Config.input_dir
    • Config.input_seq_path
    • Config.log_level
    • Config.model_attc_name
    • Config.model_attc_path
    • Config.model_dir
    • Config.model_integrase
    • Config.model_len
    • Config.model_phage_int
    • Config.outdir
    • Config.result_dir
    • Config.tmp_dir()
• hmm
  • read_hmm()
  • scan_hmm_bank()
• infernal
  • expand()
  • find_attc()
  • local_max()
  • read_infernal()
• integrase
  • find_integrase()
• integron
  • Integron
    • Integron.__init__()
    • Integron.__weakref__
    • Integron.add_attC()
    • Integron.add_attI()
    • Integron.add_integrase()
    • Integron.add_promoter()
    • Integron.add_proteins()
    • Integron.describe()
    • Integron.draw_integron()
    • Integron.has_attC()
    • Integron.has_integrase()
    • Integron.type()
  • find_integron()
• prot_db
  • GembaseDB
    • GembaseDB.__getitem__()
    • GembaseDB.__init__()
    • GembaseDB.__iter__()
    • GembaseDB._make_protfile()
    • GembaseDB._parse_lst()
    • GembaseDB.coding_prot_ids()
    • GembaseDB.find_gembase_file_basename()
    • GembaseDB.gembase1_complete_parser()
    • GembaseDB.gembase1_draft_parser()
    • GembaseDB.gembase2_parser()
    • GembaseDB.gembase_sniffer()
    • GembaseDB.get_description()
    • GembaseDB.get_lst_dir()
    • GembaseDB.get_replicon_type()
  • ProdigalDB
    • ProdigalDB.__getitem__()
    • ProdigalDB.__iter__()
    • ProdigalDB._make_protfile()
    • ProdigalDB.coding_prot_ids()
    • ProdigalDB.get_description()
  • ProteinDB
    • ProteinDB.__getitem__()
    • ProteinDB.__init__()
    • ProteinDB.__iter__()
    • ProteinDB.__weakref__
    • ProteinDB._make_db()
    • ProteinDB._make_protfile()
    • ProteinDB.coding_prot_ids()
    • ProteinDB.get_description()
    • ProteinDB.is_pseudo_gene()
    • ProteinDB.protfile
  • SeqDesc
    • SeqDesc.__getnewargs__()
    • SeqDesc.__new__()
    • SeqDesc.__replace__()
    • SeqDesc.__repr__()
    • SeqDesc._asdict()
    • SeqDesc._make()
    • SeqDesc._replace()
    • SeqDesc.id
    • SeqDesc.start
    • SeqDesc.stop
    • SeqDesc.strand
• results
  • _log
  • filter_calin()
  • integrons_report()
  • merge_results()
  • summary()
• topology
  • Topology
    • Topology.__getitem__()
    • Topology.__init__()
    • Topology.__weakref__
    • Topology._gembase_replicon_default_topo()
    • Topology._parse()
    • Topology._parse_topology()
• utils
  • FastaIterator
    • FastaIterator.__init__()
    • FastaIterator.__len__()
    • FastaIterator.__next__()
    • FastaIterator.__weakref__
    • FastaIterator._check_seq_alphabet_compliance()
    • FastaIterator._set_topologies()
  • MultiFastaReader
    • MultiFastaReader.__init__()
    • MultiFastaReader.__next__()
    • MultiFastaReader.__weakref__
    • MultiFastaReader.close()
  • get_name_from_path()
  • log_level()
  • model_len()