Index

_

_affect_canonical_ss() (src.seqvar.auto_bp7.AutoBP7 method) _affect_spliceAI() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _affect_splicing() (src.seqvar.auto_ps1_pm5.AutoPS1PM5 method) _ba1_exception() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) _bp3_not_applicable() (src.seqvar.auto_pm4_bp3.AutoPM4BP3 method) _bs2_not_applicable() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) _calc_alt_reg() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) _calc_cds() (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method) _check_zyg() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) _closest_alt_start_cdn() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) _convert_consequence() (src.seqvar.auto_pvs1.AutoPVS1 method) _count_lof_vars() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method) _count_pathogenic_vars() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method) _count_vars() (src.seqvar.auto_pm1.AutoPM1 method) _find_aff_exon_pos() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) _get_af() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) _get_affected_exon() (src.seqvar.auto_pm1.AutoPM1 method) _get_allele_cond() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) _get_any_af() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) _get_conseq() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method)

_get_control_af() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) _get_m_af() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) _get_missense_vars() (src.seqvar.auto_pp2_bp1.AutoPP2BP1 method) _get_uniprot_domain() (src.seqvar.auto_pm1.AutoPM1 method) _get_var_info() (src.seqvar.auto_ps1_pm5.AutoPS1PM5 method) _get_variant_from_range() (src.api.reev.annonars.AnnonarsClient method) _in_repeat_region() (src.seqvar.auto_pm4_bp3.AutoPM4BP3 method) _is_benign_score() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _is_benign_splicing() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _is_bp7_exception() (src.seqvar.auto_bp7.AutoBP7 method) _is_conserved() (src.seqvar.auto_bp7.AutoBP7 method) _is_inframe_indel() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _is_intron_variant() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _is_intronic() (src.seqvar.auto_bp7.AutoBP7 method) _is_missense() (src.seqvar.auto_pp2_bp1.AutoPP2BP1 method) (src.seqvar.auto_ps1_pm5.AutoPS1PM5 method) _is_missense_variant() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _is_pathogenic() (src.seqvar.auto_ps1_pm5.AutoPS1PM5 method) _is_pathogenic_score() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _is_pathogenic_splicing() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _is_splice_affecting() (src.seqvar.auto_ps1_pm5.AutoPS1PM5 method) _is_splice_variant() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _is_stop_loss() (src.seqvar.auto_pm4_bp3.AutoPM4BP3 method) _is_synonymous() (src.seqvar.auto_bp7.AutoBP7 method) _is_synonymous_variant() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _is_utr_variant() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) _minimal_deletion() (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method) _parse_HGVSp() (src.seqvar.auto_ps1_pm5.AutoPS1PM5 method) _skipping_exon_pos() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) _spliceai_impact() (src.seqvar.auto_bp7.AutoBP7 method)

A

alt_start_cdn() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) ANNONARS_API_BASE_URL (in module src.api.reev.annonars) annonars_client (src.seqvar.auto_bp7.AutoBP7 attribute) (src.seqvar.auto_pm1.AutoPM1 attribute) (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 attribute) (src.seqvar.auto_pm4_bp3.AutoPM4BP3 attribute) (src.seqvar.auto_pp2_bp1.AutoPP2BP1 attribute) (src.seqvar.auto_pp3_bp4.AutoPP3BP4 attribute) (src.seqvar.auto_ps1_pm5.AutoPS1PM5 attribute) (src.seqvar.auto_pvs1.AutoPVS1 attribute) (src.seqvar.auto_pvs1.SeqVarPVS1Helper attribute) (src.strucvar.auto_pvs1.AutoPVS1 attribute) (src.strucvar.auto_pvs1.StrucVarHelper attribute)

AnnonarsClient (class in src.api.reev.annonars) api_base_url (src.api.reev.annonars.AnnonarsClient attribute) (src.api.reev.dotty.DottyClient attribute) (src.api.reev.mehari.MehariClient attribute) AutoBP7 (class in src.seqvar.auto_bp7) AutoPM1 (class in src.seqvar.auto_pm1) AutoPM2BA1BS1BS2 (class in src.seqvar.auto_pm2_ba1_bs1_bs2) AutoPM4BP3 (class in src.seqvar.auto_pm4_bp3) AutoPP2BP1 (class in src.seqvar.auto_pp2_bp1) AutoPP3BP4 (class in src.seqvar.auto_pp3_bp4) AutoPS1PM5 (class in src.seqvar.auto_ps1_pm5) AutoPVS1 (class in src.seqvar.auto_pvs1) (class in src.strucvar.auto_pvs1)

C

cache (src.api.reev.annonars.AnnonarsClient attribute) (src.api.reev.dotty.DottyClient attribute) (src.api.reev.mehari.MehariClient attribute) client (src.api.reev.annonars.AnnonarsClient attribute) (src.api.reev.dotty.DottyClient attribute) (src.api.reev.mehari.MehariClient attribute) comment_bp7 (src.seqvar.auto_bp7.AutoBP7 attribute) comment_pm1 (src.seqvar.auto_pm1.AutoPM1 attribute) comment_pm2ba1bs1bs2 (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 attribute) comment_pm4bp3 (src.seqvar.auto_pm4_bp3.AutoPM4BP3 attribute) comment_pp2bp1 (src.seqvar.auto_pp2_bp1.AutoPP2BP1 attribute) comment_pp3bp4 (src.seqvar.auto_pp3_bp4.AutoPP3BP4 attribute) comment_ps1pm5 (src.seqvar.auto_ps1_pm5.AutoPS1PM5 attribute) comment_pvs1 (src.seqvar.auto_pvs1.AutoPVS1 attribute) (src.seqvar.auto_pvs1.SeqVarPVS1Helper attribute) (src.strucvar.auto_pvs1.AutoPVS1 attribute) (src.strucvar.auto_pvs1.StrucVarHelper attribute)

config (src.seqvar.auto_bp7.AutoBP7 attribute) (src.seqvar.auto_pm1.AutoPM1 attribute) (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 attribute) (src.seqvar.auto_pm4_bp3.AutoPM4BP3 attribute) (src.seqvar.auto_pp2_bp1.AutoPP2BP1 attribute) (src.seqvar.auto_pp3_bp4.AutoPP3BP4 attribute) (src.seqvar.auto_ps1_pm5.AutoPS1PM5 attribute) (src.seqvar.auto_pvs1.AutoPVS1 attribute) (src.seqvar.auto_pvs1.SeqVarPVS1Helper attribute) (src.strucvar.auto_pvs1.AutoPVS1 attribute) (src.strucvar.auto_pvs1.StrucVarHelper attribute) crit4prot_func() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method) CUSTOM_VCEP_PVS1 (in module src.seqvar.auto_pvs1)

D

del_disrupt_rf() (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method) DNA_BASES (in module src.seqvar.auto_ps1_pm5)

DOTTI_API_BASE_URL (in module src.api.reev.dotty) DottyClient (class in src.api.reev.dotty) dup_disrupt_rf() (src.strucvar.auto_pvs1.AutoPVS1 static method) (src.strucvar.auto_pvs1.StrucVarHelper static method)

E

exon_skip_or_cryptic_ss_disrupt() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method)

F

full_gene_del() (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method)

G

get_gene_info() (src.api.reev.annonars.AnnonarsClient method) get_gene_transcripts() (src.api.reev.mehari.MehariClient method) get_seqvar_transcripts() (src.api.reev.mehari.MehariClient method)

get_strucvar_transcripts() (src.api.reev.mehari.MehariClient method) get_variant_from_range() (src.api.reev.annonars.AnnonarsClient method) get_variant_info() (src.api.reev.annonars.AnnonarsClient method)

I

in_bio_relevant_tsx() (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method)

in_bio_relevant_tx() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) is_inframe_delins() (src.seqvar.auto_pm4_bp3.AutoPM4BP3 method)

L

lof_freq_in_pop() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method)

lof_rm_gt_10pct_of_prot() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method)

M

MEHARI_API_BASE_URL (in module src.api.reev.mehari) MehariClient (class in src.api.reev.mehari) module src.api.reev.annonars src.api.reev.dotty src.api.reev.mehari src.seqvar.auto_bp7 src.seqvar.auto_pm1 src.seqvar.auto_pm2_ba1_bs1_bs2 src.seqvar.auto_pm4_bp3 src.seqvar.auto_pp2_bp1 src.seqvar.auto_pp3_bp4 src.seqvar.auto_ps1_pm5 src.seqvar.auto_pvs1 src.strucvar.auto_pvs1

P

predict_bp7() (src.seqvar.auto_bp7.AutoBP7 method) predict_pm1() (src.seqvar.auto_pm1.AutoPM1 method) predict_pm2ba1bs1bs2() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) predict_pm4bp3() (src.seqvar.auto_pm4_bp3.AutoPM4BP3 method) predict_pp2bp1() (src.seqvar.auto_pp2_bp1.AutoPP2BP1 method) predict_pp3bp4() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) predict_ps1pm5() (src.seqvar.auto_ps1_pm5.AutoPS1PM5 method) predict_pvs1() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.AutoPVS1 method) prediction_bp7 (src.seqvar.auto_bp7.AutoBP7 attribute)

prediction_pm1 (src.seqvar.auto_pm1.AutoPM1 attribute) prediction_pm2ba1bs1bs2 (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 attribute) prediction_pm4bp3 (src.seqvar.auto_pm4_bp3.AutoPM4BP3 attribute) prediction_pp2bp1 (src.seqvar.auto_pp2_bp1.AutoPP2BP1 attribute) prediction_pp3bp4 (src.seqvar.auto_pp3_bp4.AutoPP3BP4 attribute) prediction_ps1pm5 (src.seqvar.auto_ps1_pm5.AutoPS1PM5 attribute) presumed_in_tandem() (src.strucvar.auto_pvs1.AutoPVS1 static method) (src.strucvar.auto_pvs1.StrucVarHelper static method) proven_in_tandem() (src.strucvar.auto_pvs1.AutoPVS1 static method) (src.strucvar.auto_pvs1.StrucVarHelper static method)

R

REGEX_HGVSP (in module src.seqvar.auto_ps1_pm5)

S

SeqVarPVS1Helper (class in src.seqvar.auto_pvs1) src.api.reev.annonars module src.api.reev.dotty module src.api.reev.mehari module src.seqvar.auto_bp7 module src.seqvar.auto_pm1 module src.seqvar.auto_pm2_ba1_bs1_bs2 module

src.seqvar.auto_pm4_bp3 module src.seqvar.auto_pp2_bp1 module src.seqvar.auto_pp3_bp4 module src.seqvar.auto_ps1_pm5 module src.seqvar.auto_pvs1 module src.strucvar.auto_pvs1 module StrucVarHelper (class in src.strucvar.auto_pvs1)

T

to_spdi() (src.api.reev.dotty.DottyClient method)

U

undergo_nmd() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method) (src.strucvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.StrucVarHelper method)

up_pathogenic_vars() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.seqvar.auto_pvs1.SeqVarPVS1Helper method)

V

verify_bp7() (src.seqvar.auto_bp7.AutoBP7 method) verify_pm1() (src.seqvar.auto_pm1.AutoPM1 method) verify_pm2ba1bs1bs2() (src.seqvar.auto_pm2_ba1_bs1_bs2.AutoPM2BA1BS1BS2 method) verify_pm4bp3() (src.seqvar.auto_pm4_bp3.AutoPM4BP3 method)

verify_pp2bp1() (src.seqvar.auto_pp2_bp1.AutoPP2BP1 method) verify_pp3bp4() (src.seqvar.auto_pp3_bp4.AutoPP3BP4 method) verify_ps1pm5() (src.seqvar.auto_ps1_pm5.AutoPS1PM5 method) verify_pvs1() (src.seqvar.auto_pvs1.AutoPVS1 method) (src.strucvar.auto_pvs1.AutoPVS1 method)