Index

_

__getitem__() (integron_finder.prot_db.GembaseDB method) (integron_finder.prot_db.ProdigalDB method) (integron_finder.prot_db.ProteinDB method) (integron_finder.topology.Topology method) __getnewargs__() (integron_finder.prot_db.SeqDesc method) __init__() (integron_finder.config.Config method) (integron_finder.integron.Integron method) (integron_finder.prot_db.GembaseDB method) (integron_finder.prot_db.ProteinDB method) (integron_finder.topology.Topology method) (integron_finder.utils.FastaIterator method) __iter__() (integron_finder.prot_db.GembaseDB method) (integron_finder.prot_db.ProdigalDB method) (integron_finder.prot_db.ProteinDB method) __len__() (integron_finder.utils.FastaIterator method) __new__() (integron_finder.prot_db.SeqDesc static method) __next__() (integron_finder.utils.FastaIterator method) __repr__() (integron_finder.prot_db.SeqDesc method)

__weakref__ (integron_finder.config.Config attribute) (integron_finder.integron.Integron attribute) (integron_finder.prot_db.ProteinDB attribute) (integron_finder.topology.Topology attribute) (integron_finder.utils.FastaIterator attribute) _asdict() (integron_finder.prot_db.SeqDesc method) _check_seq_alphabet_compliance() (integron_finder.utils.FastaIterator method) _gembase_replicon_default_topo() (integron_finder.topology.Topology method) _log (in module integron_finder.results) _make() (integron_finder.prot_db.SeqDesc class method) _make_db() (integron_finder.prot_db.ProteinDB method) _make_protfile() (integron_finder.prot_db.GembaseDB method) (integron_finder.prot_db.ProdigalDB method) (integron_finder.prot_db.ProteinDB method) _parse() (integron_finder.topology.Topology method) _parse_lst() (integron_finder.prot_db.GembaseDB method) _parse_topology() (integron_finder.topology.Topology method) _replace() (integron_finder.prot_db.SeqDesc method) _set_topologies() (integron_finder.utils.FastaIterator method)

A

add_attC() (integron_finder.integron.Integron method) add_attI() (integron_finder.integron.Integron method) add_feature() (in module integron_finder.annotation)

add_integrase() (integron_finder.integron.Integron method) add_promoter() (integron_finder.integron.Integron method) add_proteins() (integron_finder.integron.Integron method)

C

Config (class in integron_finder.config)

D

default_topology (integron_finder.config.Config property)

describe() (integron_finder.integron.Integron method) draw_integron() (integron_finder.integron.Integron method)

E

expand() (in module integron_finder.infernal)

F

FastaIterator (class in integron_finder.utils) filter_calin() (in module integron_finder.results) find_attc() (in module integron_finder.infernal) find_attc_max() (in module integron_finder.attc)

find_gembase_file_basename() (integron_finder.prot_db.GembaseDB class method) find_integrase() (in module integron_finder.integrase) find_integron() (in module integron_finder.integron) func_annot() (in module integron_finder.annotation) func_annot_path (integron_finder.config.Config property)

G

gembase1_complete_parser() (integron_finder.prot_db.GembaseDB static method) gembase1_draft_parser() (integron_finder.prot_db.GembaseDB static method) gembase2_parser() (integron_finder.prot_db.GembaseDB static method) gembase_sniffer() (integron_finder.prot_db.GembaseDB class method) GembaseDB (class in integron_finder.prot_db)

get_description() (integron_finder.prot_db.GembaseDB method) (integron_finder.prot_db.ProdigalDB method) (integron_finder.prot_db.ProteinDB method) get_lst_dir() (integron_finder.prot_db.GembaseDB static method) get_name_from_path() (in module integron_finder.utils) get_replicon_type() (integron_finder.prot_db.GembaseDB class method)

H

has_attC() (integron_finder.integron.Integron method)

has_integrase() (integron_finder.integron.Integron method)

I

id (integron_finder.prot_db.SeqDesc attribute) input_dir (integron_finder.config.Config property) input_seq_path (integron_finder.config.Config property) Integron (class in integron_finder.integron) integron_finder.annotation module integron_finder.attc module integron_finder.config module integron_finder.hmm module integron_finder.infernal module

integron_finder.integrase module integron_finder.integron module integron_finder.prot_db module integron_finder.results module integron_finder.topology module integron_finder.utils module integrons_report() (in module integron_finder.results)

L

local_max() (in module integron_finder.infernal)

log_level (integron_finder.config.Config property) log_level() (in module integron_finder.utils)

M

make_multi_fasta_reader() (in module integron_finder.utils) merge_results() (in module integron_finder.results) model_attc_name (integron_finder.config.Config property) model_attc_path (integron_finder.config.Config property) model_dir (integron_finder.config.Config property) model_integrase (integron_finder.config.Config property) model_len (integron_finder.config.Config property) model_len() (in module integron_finder.utils) model_phage_int (integron_finder.config.Config property) module integron_finder.annotation integron_finder.attc integron_finder.config integron_finder.hmm integron_finder.infernal integron_finder.integrase integron_finder.integron integron_finder.prot_db integron_finder.results integron_finder.topology integron_finder.utils

O

outdir (integron_finder.config.Config property)

P

ProdigalDB (class in integron_finder.prot_db)

ProteinDB (class in integron_finder.prot_db) protfile (integron_finder.prot_db.ProteinDB property)

R

read_hmm() (in module integron_finder.hmm) read_infernal() (in module integron_finder.infernal)

read_multi_fasta() (in module integron_finder.utils) result_dir (integron_finder.config.Config property)

S

scan_hmm_bank() (in module integron_finder.hmm) search_attc() (in module integron_finder.attc) SeqDesc (class in integron_finder.prot_db)

start (integron_finder.prot_db.SeqDesc attribute) stop (integron_finder.prot_db.SeqDesc attribute) strand (integron_finder.prot_db.SeqDesc attribute) summary() (in module integron_finder.results)

T

tmp_dir() (integron_finder.config.Config method)

Topology (class in integron_finder.topology) type() (integron_finder.integron.Integron method)