Index

_

__init__() (gecco.crf.ClusterCRF method) (gecco.hmmer.DomainAnnotator method) (gecco.model.ClusterType method) (gecco.orf.PyrodigalFinder method) (gecco.refine.ClusterRefiner method) (gecco.types.TypeClassifier method)

A

average_probability (gecco.model.Cluster property) (gecco.model.Gene property)

C

Cluster (class in gecco.model) cluster_weight (gecco.model.Domain attribute) ClusterCRF (class in gecco.crf)

ClusterRefiner (class in gecco.refine) ClusterTable (class in gecco.model) ClusterType (class in gecco.model)

D

Domain (class in gecco.model) domain_composition() (gecco.model.Cluster method)

DomainAnnotator (class in gecco.hmmer) domains (gecco.model.Protein attribute)

E

embedded_hmms() (in module gecco.hmmer) end (gecco.model.Cluster property) (gecco.model.Domain attribute) (gecco.model.Gene attribute)

F

FeatureTable (class in gecco.model) find_genes() (gecco.orf.ORFFinder method) (gecco.orf.PyrodigalFinder method)

fit() (gecco.crf.ClusterCRF method) from_clusters() (gecco.model.ClusterTable class method) from_genes() (gecco.model.FeatureTable class method) functions() (gecco.model.Gene method)

G

gecco.crf module gecco.hmmer module gecco.interpro module gecco.model module gecco.orf module

gecco.refine module gecco.types module Gene (class in gecco.model) genes (gecco.model.Cluster attribute) go_functions (gecco.model.Domain attribute) go_terms (gecco.model.Domain attribute)

H

HMM (class in gecco.hmmer)

hmm (gecco.model.Domain attribute)

I

i_evalue (gecco.model.Domain attribute) id (gecco.hmmer.HMM attribute) (gecco.model.Cluster attribute) (gecco.model.Gene property) (gecco.model.Protein attribute)

InterPro (class in gecco.interpro) InterProEntry (class in gecco.interpro) inverse_transform() (gecco.types.TypeBinarizer method) iter_clusters() (gecco.refine.ClusterRefiner method)

M

maximum_probability (gecco.model.Cluster property) (gecco.model.Gene property) md5 (gecco.hmmer.HMM attribute) module gecco.crf gecco.hmmer gecco.interpro gecco.model gecco.orf gecco.refine gecco.types

N

name (gecco.model.Domain attribute)

O

ORFFinder (class in gecco.orf)

P

path (gecco.hmmer.HMM attribute) predict_probabilities() (gecco.crf.ClusterCRF method) predict_types() (gecco.types.TypeClassifier method) probability (gecco.model.Domain attribute)

Protein (class in gecco.model) protein (gecco.model.Gene attribute) pvalue (gecco.model.Domain attribute) PyHMMER (class in gecco.hmmer) PyrodigalFinder (class in gecco.orf)

Q

qualifiers (gecco.model.Domain attribute) (gecco.model.Gene attribute)

R

relabel() (gecco.hmmer.HMM method) relabel_with (gecco.hmmer.HMM attribute)

run() (gecco.hmmer.DomainAnnotator method) (gecco.hmmer.PyHMMER method)

S

save() (gecco.crf.ClusterCRF method) seq (gecco.model.Protein attribute) sign (gecco.model.Strand property) size (gecco.hmmer.HMM attribute) source (gecco.model.Cluster property) (gecco.model.Gene attribute)

start (gecco.model.Cluster property) (gecco.model.Domain attribute) (gecco.model.Gene attribute) Strand (class in gecco.model) strand (gecco.model.Gene attribute)

T

to_genes() (gecco.model.FeatureTable method) to_seq_feature() (gecco.model.Domain method) (gecco.model.Gene method) to_seq_record() (gecco.model.Cluster method) (gecco.model.Protein method) trained() (gecco.crf.ClusterCRF class method) (gecco.types.TypeClassifier class method)

transform() (gecco.types.TypeBinarizer method) TypeBinarizer (class in gecco.types) TypeClassifier (class in gecco.types) types (gecco.model.Cluster attribute) types_probabilities (gecco.model.Cluster attribute)

U

unpack() (gecco.model.ClusterType method)

url (gecco.hmmer.HMM attribute)

V

version (gecco.hmmer.HMM attribute)

W

with_cluster_weight() (gecco.model.Domain method) with_domains() (gecco.model.Protein method) with_probability() (gecco.model.Domain method) (gecco.model.Gene method)

with_protein() (gecco.model.Gene method) with_seq() (gecco.model.Protein method) with_source() (gecco.model.Gene method)