Index

A

as_matrix() (gepyto.formats.impute2.Impute2File method)

as_range() (gepyto.structures.region.Region method)

B

base_base_correlation() (gepyto.structures.sequences.Sequence method) bbc() (gepyto.structures.sequences.Sequence method)

build_index() (in module gepyto.db.index)

C

check_indel_reference() (in module gepyto.reference) check_snp_reference() (in module gepyto.reference)

check_variant_reference() (gepyto.reference.Reference method)

D

distance_to() (gepyto.structures.region.Region method)

E

ensembl_genes_in_region() (in module gepyto.utils.genes)

ensembl_variants_in_region() (in module gepyto.utils.variants)

F

factory_ensembl_id() (gepyto.structures.genes.Gene class method) factory_position() (gepyto.structures.genes.Transcript class method) factory_symbol() (gepyto.structures.genes.Gene class method) find_coding_sequences() (gepyto.structures.sequences.Sequence method)

find_translations() (gepyto.structures.sequences.Sequence method) from_ensembl_api() (gepyto.structures.variants.Indel class method) (gepyto.structures.variants.SNP class method) from_reference() (gepyto.structures.sequences.Sequence class method) from_str() (gepyto.structures.region.Region static method) (gepyto.structures.variants.SNP class method)

G

gc_content() (gepyto.structures.sequences.Sequence method) Gene (class in gepyto.structures.genes) gepyto.db.appris (module) gepyto.db.ensembl (module) gepyto.db.index (module) gepyto.db.ucsc (module) gepyto.formats.gtf (module) gepyto.formats.impute2 (module) gepyto.formats.seqxml (module) gepyto.formats.wig (module) gepyto.reference (module) gepyto.structures.genes (module) gepyto.structures.region (module) gepyto.structures.sequences (module) gepyto.structures.variants (module) gepyto.utils.genes (module) gepyto.utils.variants (module) get_annotations() (gepyto.structures.sequences.Sequence method) get_category_for_transcript() (in module gepyto.db.appris)

get_centromere() (in module gepyto.db.ucsc) get_index() (in module gepyto.db.index) get_main_transcripts() (in module gepyto.db.appris) get_nucleotide() (gepyto.reference.Reference method) get_ortholog_sequences() (gepyto.structures.genes.Gene method) get_paralog_sequences() (gepyto.structures.genes.Gene method) get_phylop_100_way() (in module gepyto.db.ucsc) get_seq() (gepyto.formats.seqxml.SeqXML method) get_sequence() (gepyto.reference.Reference method) (gepyto.structures.genes.Transcript method) get_telomere() (in module gepyto.db.ucsc) get_transcripts_for_gene() (in module gepyto.db.appris) get_url_prefix() (in module gepyto.db.ensembl) get_xrefs() (gepyto.structures.genes.Gene class method) get_xrefs_from_ensembl_id() (gepyto.structures.genes.Gene class method) get_xrefs_from_symbol() (gepyto.structures.genes.Gene class method) GFFFile (in module gepyto.formats.gtf) goto() (in module gepyto.db.index) GTFFile (class in gepyto.formats.gtf)

I

Impute2File (class in gepyto.formats.impute2) Indel (class in gepyto.structures.variants)

init_db() (in module gepyto.db.appris) InvalidMapping

L

length (gepyto.structures.variants.Indel attribute)

Line (gepyto.formats.gtf.GTFFile attribute)

M

maketrans() (in module gepyto.structures.sequences)

O

overlaps_with() (gepyto.structures.region.Region method)

Q

query_ensembl() (in module gepyto.db.ensembl)

query_gap_table() (gepyto.db.ucsc.UCSC method)

R

raw_sql() (gepyto.db.ucsc.UCSC method) readline() (gepyto.formats.impute2.Impute2File method) Reference (class in gepyto.reference)

Region (class in gepyto.structures.region) region (gepyto.structures.genes.Gene attribute) (gepyto.structures.genes.Transcript attribute) reverse_complement() (gepyto.structures.sequences.Sequence method)

S

Sequence (class in gepyto.structures.sequences) sequence (gepyto.structures.region.Region attribute) SeqXML (class in gepyto.formats.seqxml)

smith_waterman() (in module gepyto.structures.sequences) SNP (class in gepyto.structures.variants)

T

to_fasta() (gepyto.structures.sequences.Sequence method) Transcript (class in gepyto.structures.genes)

translate() (gepyto.structures.sequences.Sequence method)

U

UCSC (class in gepyto.db.ucsc)

union() (gepyto.structures.region.Region method)

V

variant_list_to_dataframe() (in module gepyto.structures.variants)

W

WiggleFile (class in gepyto.formats.wig)