Index _ | A | B | C | D | E | G | I | L | M | N | P | R | S | T | U | V | W | Z _ __init__() (cool_seq_tool.app.CoolSeqTool method) (cool_seq_tool.data.data_downloads.DataDownload method) (cool_seq_tool.mappers.alignment.AlignmentMapper method) (cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper method) (cool_seq_tool.mappers.mane_transcript.ManeTranscript method) (cool_seq_tool.sources.mane_transcript_mappings.ManeTranscriptMappings method) (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) (cool_seq_tool.sources.uta_database.UtaDatabase method) A ac_to_chromosome() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) AlignmentMapper (class in cool_seq_tool.mappers.alignment) alt_ac (cool_seq_tool.mappers.mane_transcript.CdnaRepresentation attribute) (cool_seq_tool.mappers.mane_transcript.GenomicRepresentation attribute) (cool_seq_tool.schemas.MappedManeData attribute) AnnotationLayer (class in cool_seq_tool.schemas) Assembly (class in cool_seq_tool.schemas) assembly (cool_seq_tool.schemas.MappedManeData attribute) B BaseModelForbidExtra (class in cool_seq_tool.schemas) C c_ac (cool_seq_tool.schemas.CdnaRepresentation attribute) c_data (cool_seq_tool.schemas.ToCdnaService attribute) c_end_pos (cool_seq_tool.schemas.CdnaRepresentation attribute) c_start_pos (cool_seq_tool.schemas.CdnaRepresentation attribute) c_to_g() (cool_seq_tool.mappers.alignment.AlignmentMapper method) CDNA (cool_seq_tool.mappers.mane_transcript.EndAnnotationLayer attribute) cdna (cool_seq_tool.mappers.mane_transcript.ProteinAndCdnaRepresentation attribute) CDNA (cool_seq_tool.schemas.AnnotationLayer attribute) CdnaRepresentation (class in cool_seq_tool.mappers.mane_transcript) (class in cool_seq_tool.schemas) cds_start (cool_seq_tool.schemas.CdnaRepresentation attribute) check_exon_start_and_exon_end() (cool_seq_tool.schemas.TranscriptRequestBody class method) check_start_and_end() (cool_seq_tool.schemas.GenomicRequestBody class method) check_start_end() (cool_seq_tool.schemas.GenomicData class method) chr (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.TranscriptExonData attribute) chromosome (cool_seq_tool.schemas.GenomicRequestBody attribute) chromosome_to_acs() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) coding_dna_transcripts() (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) coding_end_site (cool_seq_tool.mappers.mane_transcript.CdnaRepresentation attribute) coding_start_site (cool_seq_tool.mappers.mane_transcript.CdnaRepresentation attribute) cool_seq_tool.app module cool_seq_tool.data.data_downloads module cool_seq_tool.handlers.seqrepo_access module cool_seq_tool.mappers.alignment module cool_seq_tool.mappers.exon_genomic_coords module cool_seq_tool.mappers.mane_transcript module cool_seq_tool.schemas module cool_seq_tool.sources.mane_transcript_mappings module cool_seq_tool.sources.transcript_mappings module cool_seq_tool.sources.uta_database module cool_seq_tool.utils module CoolSeqTool (class in cool_seq_tool.app) create() (cool_seq_tool.sources.uta_database.UtaDatabase class method) create_pool() (cool_seq_tool.sources.uta_database.UtaDatabase method) D data_from_result() (cool_seq_tool.sources.uta_database.UtaDatabase static method) database (cool_seq_tool.sources.uta_database.ParseResult property) DataDownload (class in cool_seq_tool.data.data_downloads) DataRepresentation (class in cool_seq_tool.mappers.mane_transcript) E end (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.GenomicRequestBody attribute) EndAnnotationLayer (class in cool_seq_tool.mappers.mane_transcript) ensembl (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.schemas.ManeData attribute) (cool_seq_tool.schemas.MappedManeData attribute) execute_query() (cool_seq_tool.sources.uta_database.UtaDatabase method) exon (cool_seq_tool.schemas.TranscriptExonData attribute) exon_end (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.TranscriptRequestBody attribute) exon_end_offset (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.TranscriptRequestBody attribute) exon_offset (cool_seq_tool.schemas.TranscriptExonData attribute) exon_start (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.TranscriptRequestBody attribute) exon_start_offset (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.TranscriptRequestBody attribute) ExonGenomicCoordsMapper (class in cool_seq_tool.mappers.exon_genomic_coords) G g_ac (cool_seq_tool.schemas.GenomicRepresentation attribute) g_data (cool_seq_tool.schemas.ToGenomicService attribute) g_end_pos (cool_seq_tool.schemas.GenomicRepresentation attribute) g_start_pos (cool_seq_tool.schemas.GenomicRepresentation attribute) g_to_grch38() (cool_seq_tool.mappers.mane_transcript.ManeTranscript method) g_to_mane_c() (cool_seq_tool.mappers.mane_transcript.ManeTranscript method) gene (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.GenomicRequestBody attribute) (cool_seq_tool.schemas.ManeData attribute) (cool_seq_tool.schemas.MappedManeData attribute) (cool_seq_tool.schemas.TranscriptExonData attribute) (cool_seq_tool.schemas.TranscriptRequestBody attribute) GENOMIC (cool_seq_tool.schemas.AnnotationLayer attribute) genomic_data (cool_seq_tool.schemas.GenomicDataResponse attribute) genomic_to_transcript_exon_coordinates() (cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper method) GenomicData (class in cool_seq_tool.schemas) GenomicDataResponse (class in cool_seq_tool.schemas) GenomicRepresentation (class in cool_seq_tool.mappers.mane_transcript) (class in cool_seq_tool.schemas) GenomicRequestBody (class in cool_seq_tool.schemas) get_ac_descr() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_ac_from_gene() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_alt_ac_start_or_end() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_cds_start_end() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_chr_assembly() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_fasta_file() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) get_gene_from_ac() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_gene_mane_data() (cool_seq_tool.sources.mane_transcript_mappings.ManeTranscriptMappings method) get_gene_symbol_from_ensembl_protein() (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) get_gene_symbol_from_ensembl_transcript() (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) get_gene_symbol_from_refeq_protein() (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) get_gene_symbol_from_refseq_rna() (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) get_genes_and_alt_acs() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_genomic_tx_data() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_inter_residue_pos() (in module cool_seq_tool.utils) get_liftover() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_longest_compatible_transcript() (cool_seq_tool.mappers.mane_transcript.ManeTranscript method) get_lrg_refseq_gene_data() (cool_seq_tool.data.data_downloads.DataDownload method) get_mane_c_genomic_data() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_mane_c_pos_change() (cool_seq_tool.mappers.mane_transcript.ManeTranscript static method) get_mane_data_from_chr_pos() (cool_seq_tool.sources.mane_transcript_mappings.ManeTranscriptMappings method) get_mane_from_transcripts() (cool_seq_tool.sources.mane_transcript_mappings.ManeTranscriptMappings method) get_mane_summary() (cool_seq_tool.data.data_downloads.DataDownload method) get_mane_transcript() (cool_seq_tool.mappers.mane_transcript.ManeTranscript method) get_newest_assembly_ac() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_reference_sequence() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) get_secret() (cool_seq_tool.sources.uta_database.UtaDatabase static method) get_transcripts() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_transcripts_from_genomic_pos() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_tx_exon_aln_v_data() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_tx_exon_coords() (cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper method) get_tx_exons() (cool_seq_tool.sources.uta_database.UtaDatabase method) get_tx_exons_genomic_coords() (cool_seq_tool.sources.uta_database.UtaDatabase method) GRCH37 (cool_seq_tool.schemas.Assembly attribute) GRCH38 (cool_seq_tool.schemas.Assembly attribute) (cool_seq_tool.schemas.TranscriptPriority attribute) grch38_to_mane_c_p() (cool_seq_tool.mappers.mane_transcript.ManeTranscript method) I INTER_RESIDUE (cool_seq_tool.schemas.ResidueMode attribute) L liftover_to_38() (cool_seq_tool.sources.uta_database.UtaDatabase method) LONGEST_COMPATIBLE_REMAINING (cool_seq_tool.schemas.TranscriptPriority attribute) M mane_data (cool_seq_tool.schemas.ManeDataService attribute) MANE_PLUS_CLINICAL (cool_seq_tool.schemas.TranscriptPriority attribute) MANE_SELECT (cool_seq_tool.schemas.TranscriptPriority attribute) ManeData (class in cool_seq_tool.schemas) ManeDataService (class in cool_seq_tool.schemas) ManeTranscript (class in cool_seq_tool.mappers.mane_transcript) ManeTranscriptMappings (class in cool_seq_tool.sources.mane_transcript_mappings) mapped_mane_data (cool_seq_tool.schemas.MappedManeDataService attribute) MappedManeData (class in cool_seq_tool.schemas) MappedManeDataService (class in cool_seq_tool.schemas) model_computed_fields (cool_seq_tool.mappers.mane_transcript.CdnaRepresentation attribute) (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.mappers.mane_transcript.GenomicRepresentation attribute) (cool_seq_tool.mappers.mane_transcript.ProteinAndCdnaRepresentation attribute) (cool_seq_tool.schemas.BaseModelForbidExtra attribute) (cool_seq_tool.schemas.CdnaRepresentation attribute) (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.GenomicDataResponse attribute) (cool_seq_tool.schemas.GenomicRepresentation attribute) (cool_seq_tool.schemas.GenomicRequestBody attribute) (cool_seq_tool.schemas.ManeData attribute) (cool_seq_tool.schemas.ManeDataService attribute) (cool_seq_tool.schemas.MappedManeData attribute) (cool_seq_tool.schemas.MappedManeDataService attribute) (cool_seq_tool.schemas.ServiceMeta attribute) (cool_seq_tool.schemas.ToCdnaService attribute) (cool_seq_tool.schemas.ToGenomicService attribute) (cool_seq_tool.schemas.TranscriptExonData attribute) (cool_seq_tool.schemas.TranscriptExonDataResponse attribute) (cool_seq_tool.schemas.TranscriptRequestBody attribute) module cool_seq_tool.app cool_seq_tool.data.data_downloads cool_seq_tool.handlers.seqrepo_access cool_seq_tool.mappers.alignment cool_seq_tool.mappers.exon_genomic_coords cool_seq_tool.mappers.mane_transcript cool_seq_tool.schemas cool_seq_tool.sources.mane_transcript_mappings cool_seq_tool.sources.transcript_mappings cool_seq_tool.sources.uta_database cool_seq_tool.utils N name (cool_seq_tool.schemas.ServiceMeta attribute) NEGATIVE (cool_seq_tool.schemas.Strand attribute) P p_to_c() (cool_seq_tool.mappers.alignment.AlignmentMapper method) p_to_c_ac() (cool_seq_tool.sources.uta_database.UtaDatabase method) p_to_g() (cool_seq_tool.mappers.alignment.AlignmentMapper method) ParseResult (class in cool_seq_tool.sources.uta_database) pos (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.mappers.mane_transcript.GenomicRepresentation attribute) (cool_seq_tool.schemas.ManeData attribute) (cool_seq_tool.schemas.TranscriptExonData attribute) POSITIVE (cool_seq_tool.schemas.Strand attribute) PROTEIN (cool_seq_tool.mappers.mane_transcript.EndAnnotationLayer attribute) protein (cool_seq_tool.mappers.mane_transcript.ProteinAndCdnaRepresentation attribute) PROTEIN (cool_seq_tool.schemas.AnnotationLayer attribute) PROTEIN_AND_CDNA (cool_seq_tool.mappers.mane_transcript.EndAnnotationLayer attribute) protein_transcripts() (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) ProteinAndCdnaRepresentation (class in cool_seq_tool.mappers.mane_transcript) R refseq (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.mappers.mane_transcript.GenomicRepresentation attribute) (cool_seq_tool.schemas.ManeData attribute) (cool_seq_tool.schemas.MappedManeData attribute) RESIDUE (cool_seq_tool.schemas.ResidueMode attribute) residue_mode (cool_seq_tool.schemas.CdnaRepresentation attribute) (cool_seq_tool.schemas.GenomicRepresentation attribute) (cool_seq_tool.schemas.GenomicRequestBody attribute) ResidueMode (class in cool_seq_tool.schemas) response_datetime (cool_seq_tool.schemas.ServiceMeta attribute) S schema (cool_seq_tool.sources.uta_database.ParseResult property) SeqRepoAccess (class in cool_seq_tool.handlers.seqrepo_access) service_meta (cool_seq_tool.schemas.GenomicDataResponse attribute) (cool_seq_tool.schemas.ManeDataService attribute) (cool_seq_tool.schemas.MappedManeDataService attribute) (cool_seq_tool.schemas.ToCdnaService attribute) (cool_seq_tool.schemas.ToGenomicService attribute) (cool_seq_tool.schemas.TranscriptExonDataResponse attribute) service_meta() (in module cool_seq_tool.utils) ServiceMeta (class in cool_seq_tool.schemas) start (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.GenomicRequestBody attribute) status (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.mappers.mane_transcript.GenomicRepresentation attribute) (cool_seq_tool.schemas.ManeData attribute) (cool_seq_tool.schemas.MappedManeData attribute) Strand (class in cool_seq_tool.schemas) strand (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.GenomicRequestBody attribute) (cool_seq_tool.schemas.ManeData attribute) (cool_seq_tool.schemas.MappedManeData attribute) (cool_seq_tool.schemas.TranscriptExonData attribute) T ToCdnaService (class in cool_seq_tool.schemas) ToGenomicService (class in cool_seq_tool.schemas) transcript (cool_seq_tool.schemas.GenomicData attribute) (cool_seq_tool.schemas.GenomicRequestBody attribute) (cool_seq_tool.schemas.TranscriptExonData attribute) (cool_seq_tool.schemas.TranscriptRequestBody attribute) transcript_exon_data (cool_seq_tool.schemas.TranscriptExonDataResponse attribute) transcript_to_genomic_coordinates() (cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper method) TranscriptExonData (class in cool_seq_tool.schemas) TranscriptExonDataResponse (class in cool_seq_tool.schemas) TranscriptMappings (class in cool_seq_tool.sources.transcript_mappings) TranscriptPriority (class in cool_seq_tool.schemas) TranscriptRequestBody (class in cool_seq_tool.schemas) translate_alias() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) translate_identifier() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) U url (cool_seq_tool.schemas.ServiceMeta attribute) UtaDatabase (class in cool_seq_tool.sources.uta_database) V validate_genomic_ac() (cool_seq_tool.sources.uta_database.UtaDatabase method) validate_version() (cool_seq_tool.schemas.ServiceMeta class method) version (cool_seq_tool.schemas.ServiceMeta attribute) W warnings (cool_seq_tool.schemas.GenomicDataResponse attribute) (cool_seq_tool.schemas.ManeDataService attribute) (cool_seq_tool.schemas.MappedManeDataService attribute) (cool_seq_tool.schemas.ToCdnaService attribute) (cool_seq_tool.schemas.ToGenomicService attribute) (cool_seq_tool.schemas.TranscriptExonDataResponse attribute) Z ZERO (cool_seq_tool.schemas.ResidueMode attribute)