Index

_

__init__() (pymlst.cla.core.ClassicalMLST method) (pymlst.cla.core.DatabaseCLA method) (pymlst.cla.core.ST_result method) (pymlst.pytyper.core.Clmt method) (pymlst.pytyper.core.FimH method) (pymlst.pytyper.core.PyTyper method) (pymlst.pytyper.core.Spa method) (pymlst.pytyper.core.TypingResult method) (pymlst.wg.core.DatabaseWG method) (pymlst.wg.core.WholeGenomeMLST method) (pymlst.wg.extractors.GeneExtractor method) (pymlst.wg.extractors.MlstExtractor method) (pymlst.wg.extractors.MsaExtractor method) (pymlst.wg.extractors.SequenceExtractor method) (pymlst.wg.extractors.StrainExtractor method) (pymlst.wg.extractors.TableExtractor method) (pymlst.wg.extractors.TableExtractorCommand method)

A

add_infos() (pymlst.cla.core.ClassicalMLST method) (pymlst.cla.core.DatabaseCLA method) (pymlst.wg.core.DatabaseWG method) (pymlst.wg.core.WholeGenomeMLST method)

add_mlst() (pymlst.cla.core.DatabaseCLA method) add_reads() (pymlst.wg.core.WholeGenomeMLST method) add_sequence() (pymlst.cla.core.DatabaseCLA method) add_sequence_strain() (pymlst.wg.extractors.MsaExtractor method) add_strain() (pymlst.wg.core.WholeGenomeMLST method)

C

check_input() (pymlst.pytyper.core.PyTyper method) check_repetition() (pymlst.pytyper.core.Spa method) ClassicalMLST (class in pymlst.cla.core) Clmt (class in pymlst.pytyper.core) close() (pymlst.pytyper.core.PyTyper method) contains_souche() (pymlst.wg.core.DatabaseWG method) count_genes_per_souche() (pymlst.wg.core.DatabaseWG method) count_sequences() (pymlst.wg.core.DatabaseWG method)

count_sequences_per_gene() (pymlst.wg.core.DatabaseWG method) count_souches_per_gene() (pymlst.wg.core.DatabaseWG method) create() (pymlst.cla.core.ClassicalMLST method) (pymlst.pytyper.core.Clmt method) (pymlst.pytyper.core.FimH method) (pymlst.pytyper.core.PyTyper method) (pymlst.pytyper.core.Spa method) (pymlst.wg.core.WholeGenomeMLST method)

D

DatabaseCLA (class in pymlst.cla.core) DatabaseWG (class in pymlst.wg.core)

DistanceExtractor (class in pymlst.wg.extractors) DuplicationHandling (class in pymlst.wg.core)

E

extract() (pymlst.wg.core.Extractor method) (pymlst.wg.core.WholeGenomeMLST method) (pymlst.wg.extractors.DistanceExtractor method) (pymlst.wg.extractors.GeneExtractor method) (pymlst.wg.extractors.MlstExtractor method) (pymlst.wg.extractors.MsaExtractor method) (pymlst.wg.extractors.SequenceExtractor method) (pymlst.wg.extractors.StatsExtractor method) (pymlst.wg.extractors.StrainExtractor method) (pymlst.wg.extractors.TableExtractor method)

Extractor (class in pymlst.wg.core)

F

FimH (class in pymlst.pytyper.core)

find_recombination() (in module pymlst.wg.core) find_subgraph() (in module pymlst.wg.core)

G

GeneExtractor (class in pymlst.wg.extractors) get_all_sequences() (pymlst.cla.core.DatabaseCLA method) get_all_sequences_by_gene() (pymlst.cla.core.DatabaseCLA method) get_all_strains() (pymlst.wg.core.DatabaseWG method) get_allele_by_sequence_and_gene() (pymlst.cla.core.DatabaseCLA method) get_core_genes() (pymlst.wg.core.DatabaseWG method) get_duplicated_genes() (pymlst.wg.core.DatabaseWG method) get_gene_sequences() (pymlst.wg.core.DatabaseWG method) get_genes_by_allele() (pymlst.cla.core.DatabaseCLA method)

get_infos() (pymlst.cla.core.ClassicalMLST method) (pymlst.cla.core.DatabaseCLA method) (pymlst.wg.core.DatabaseWG method) (pymlst.wg.core.WholeGenomeMLST method) get_mlst() (pymlst.wg.core.DatabaseWG method) get_sequence_by_gene_and_allele() (pymlst.cla.core.DatabaseCLA method) get_st() (pymlst.cla.core.DatabaseCLA method) get_st_by_gene_and_allele() (pymlst.cla.core.DatabaseCLA method) get_strains_distances() (pymlst.wg.core.DatabaseWG method)

M

MlstExtractor (class in pymlst.wg.extractors) module pymlst pymlst.cla.core pymlst.pytyper.core pymlst.wg.core pymlst.wg.extractors

MsaExtractor (class in pymlst.wg.extractors) multi_read() (pymlst.cla.core.ClassicalMLST method) multi_search() (pymlst.cla.core.ClassicalMLST method) (pymlst.pytyper.core.Clmt method) (pymlst.pytyper.core.FimH method) (pymlst.pytyper.core.PyTyper method) (pymlst.pytyper.core.Spa method)

O

open_cla() (in module pymlst.cla.core)

open_typer() (in module pymlst.pytyper.core) open_wg() (in module pymlst.wg.core)

P

pymlst module pymlst.cla.core module pymlst.pytyper.core module

pymlst.wg.core module pymlst.wg.extractors module PyTyper (class in pymlst.pytyper.core)

R

remove_allele() (pymlst.cla.core.ClassicalMLST method) (pymlst.cla.core.DatabaseCLA method) remove_gene() (pymlst.wg.core.DatabaseWG method) (pymlst.wg.core.WholeGenomeMLST method)

remove_strain() (pymlst.wg.core.DatabaseWG method) (pymlst.wg.core.WholeGenomeMLST method)

S

search_genome() (pymlst.pytyper.core.Clmt method) (pymlst.pytyper.core.FimH method) (pymlst.pytyper.core.PyTyper method) (pymlst.pytyper.core.Spa method) search_read() (pymlst.cla.core.ClassicalMLST method) search_st() (pymlst.cla.core.ClassicalMLST method) SequenceExtractor (class in pymlst.wg.extractors)

set_allele() (pymlst.pytyper.core.TypingResult method) set_notes() (pymlst.pytyper.core.TypingResult method) set_st() (pymlst.pytyper.core.TypingResult method) Spa (class in pymlst.pytyper.core) ST_result (class in pymlst.cla.core) StatsExtractor (class in pymlst.wg.extractors) StrainExtractor (class in pymlst.wg.extractors)

T

TableExtractor (class in pymlst.wg.extractors)

TableExtractorCommand (class in pymlst.wg.extractors) TypingResult (class in pymlst.pytyper.core)

W

WholeGenomeMLST (class in pymlst.wg.core) write() (pymlst.cla.core.ST_result method) (pymlst.pytyper.core.TypingResult method)

write_fasta_allele() (pymlst.pytyper.core.PyTyper method)