Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V _ __init__() (cool_seq_tool.app.CoolSeqTool method) (cool_seq_tool.mappers.alignment.AlignmentMapper method) (cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper method) (cool_seq_tool.mappers.feature_overlap.FeatureOverlap method) (cool_seq_tool.mappers.liftover.LiftOver 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.LazyUtaDatabase method) (cool_seq_tool.sources.uta_database.UtaDatabase method) (cool_seq_tool.sources.uta_database.UtaRepository method) A ac (cool_seq_tool.mappers.mane_transcript.GenomicRepresentation attribute) ac_to_chromosome() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) add_meta_check_errors() (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService class method) AlignmentMapper (class in cool_seq_tool.mappers.alignment) alt_ac (cool_seq_tool.mappers.mane_transcript.CdnaRepresentation attribute) (cool_seq_tool.schemas.GenomicTxMetadata attribute) (cool_seq_tool.sources.uta_database.GenomicAlnData attribute) alt_aln_method (cool_seq_tool.schemas.GenomicTxData attribute) (cool_seq_tool.sources.uta_database.TxExonAlnData attribute) alt_end_i (cool_seq_tool.sources.uta_database.ExonCoord attribute) (cool_seq_tool.sources.uta_database.GenomicAlnData attribute) alt_exon_id (cool_seq_tool.schemas.GenomicTxData attribute) (cool_seq_tool.sources.uta_database.TxExonAlnData attribute) alt_pos_change_range (cool_seq_tool.schemas.GenomicTxMetadata attribute) alt_pos_range (cool_seq_tool.schemas.GenomicTxData attribute) alt_start_i (cool_seq_tool.sources.uta_database.ExonCoord attribute) (cool_seq_tool.sources.uta_database.GenomicAlnData attribute) alt_strand (cool_seq_tool.sources.uta_database.ExonCoord attribute) (cool_seq_tool.sources.uta_database.GenomicAlnData attribute) AnnotationLayer (class in cool_seq_tool.schemas) Assembly (class in cool_seq_tool.schemas) B BaseModelForbidExtra (class in cool_seq_tool.schemas) C 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) cds (cool_seq_tool.schemas.CdsOverlap attribute) CdsOverlap (class in cool_seq_tool.schemas) check_errors() (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSeg class method) check_seg_pos() (cool_seq_tool.mappers.exon_genomic_coords.TxSegment class method) chromosome_to_acs() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) close() (cool_seq_tool.sources.uta_database.UtaDatabase method) ClosedUtaConnectionError coding_dna_transcripts() (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) coding_end_site (cool_seq_tool.mappers.mane_transcript.CdnaRepresentation attribute) (cool_seq_tool.schemas.GenomicTxMetadata attribute) coding_start_site (cool_seq_tool.mappers.mane_transcript.CdnaRepresentation attribute) (cool_seq_tool.schemas.GenomicTxMetadata attribute) cool_seq_tool.app 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.feature_overlap module cool_seq_tool.mappers.liftover module cool_seq_tool.mappers.mane_transcript module cool_seq_tool.resources.data_files 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) CoordinateType (class in cool_seq_tool.schemas) create_uta_connection_pool() (in module cool_seq_tool.sources.uta_database) D database (cool_seq_tool.sources.uta_database.ParseResult property) DataFile (class in cool_seq_tool.resources.data_files) DataRepresentation (class in cool_seq_tool.mappers.mane_transcript) E EndAnnotationLayer (class in cool_seq_tool.mappers.mane_transcript) ensembl (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) errors (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSeg attribute) (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService attribute) execute_query() (cool_seq_tool.sources.uta_database.UtaRepository method) exon_ord (cool_seq_tool.mappers.exon_genomic_coords.TxSegment attribute) ExonCoord (class in cool_seq_tool.sources.uta_database) ExonGenomicCoordsMapper (class in cool_seq_tool.mappers.exon_genomic_coords) F FeatureOverlap (class in cool_seq_tool.mappers.feature_overlap) FeatureOverlapError G 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.exon_genomic_coords.GenomicTxSeg attribute) (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService attribute) (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.schemas.GenomicTxData attribute) gene_exists() (cool_seq_tool.sources.uta_database.UtaRepository method) GENOMIC (cool_seq_tool.schemas.AnnotationLayer attribute) genomic_ac (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSeg attribute) (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService attribute) genomic_location (cool_seq_tool.mappers.exon_genomic_coords.TxSegment attribute) genomic_to_tx_segment() (cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper method) GenomicAlnData (class in cool_seq_tool.sources.uta_database) GenomicRepresentation (class in cool_seq_tool.mappers.mane_transcript) GenomicTxData (class in cool_seq_tool.schemas) GenomicTxMetadata (class in cool_seq_tool.schemas) GenomicTxSeg (class in cool_seq_tool.mappers.exon_genomic_coords) GenomicTxSegService (class in cool_seq_tool.mappers.exon_genomic_coords) get_ac_descr() (cool_seq_tool.sources.uta_database.UtaRepository method) get_ac_from_gene() (cool_seq_tool.sources.uta_database.UtaRepository method) get_all_exon_coords() (cool_seq_tool.sources.uta_database.UtaRepository method) get_alt_ac_start_or_end() (cool_seq_tool.sources.uta_database.UtaRepository method) get_alt_acs_for_tx() (cool_seq_tool.sources.uta_database.UtaRepository method) get_cds_start_end() (cool_seq_tool.sources.uta_database.UtaRepository method) get_chr_assembly() (cool_seq_tool.sources.uta_database.UtaRepository method) get_data_file() (in module cool_seq_tool.resources.data_files) get_fasta_file() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) get_gene_from_ac() (cool_seq_tool.sources.uta_database.UtaRepository method) get_gene_from_tx_ac() (cool_seq_tool.sources.uta_database.UtaRepository 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_refseq_protein() (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) get_gene_symbol_from_refseq_rna() (cool_seq_tool.sources.transcript_mappings.TranscriptMappings method) get_genomic_mane_genes() (cool_seq_tool.sources.mane_transcript_mappings.ManeTranscriptMappings method) get_genomic_tx_data() (cool_seq_tool.sources.uta_database.UtaRepository method) get_grch38_mane_gene_cds_overlap() (cool_seq_tool.mappers.feature_overlap.FeatureOverlap method) get_inter_residue_pos() (in module cool_seq_tool.utils) get_liftover() (cool_seq_tool.mappers.liftover.LiftOver method) get_longest_compatible_transcript() (cool_seq_tool.mappers.mane_transcript.ManeTranscript method) get_mane_c_genomic_data() (cool_seq_tool.sources.uta_database.UtaRepository 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_transcript() (cool_seq_tool.mappers.mane_transcript.ManeTranscript method) get_newest_assembly_ac() (cool_seq_tool.sources.uta_database.UtaRepository method) get_reading_frame() (cool_seq_tool.mappers.mane_transcript.ManeTranscript static method) get_reference_sequence() (cool_seq_tool.handlers.seqrepo_access.SeqRepoAccess method) get_transcript_status() (cool_seq_tool.sources.mane_transcript_mappings.ManeTranscriptMappings method) get_transcripts() (cool_seq_tool.sources.uta_database.UtaRepository method) get_transcripts_from_genomic_pos() (cool_seq_tool.sources.uta_database.UtaRepository method) get_tx_exon_aln_data() (cool_seq_tool.sources.uta_database.UtaRepository 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) H hgnc (cool_seq_tool.sources.uta_database.GenomicAlnData attribute) hgnc_id (cool_seq_tool.schemas.ManeGeneData attribute) I INTER_RESIDUE (cool_seq_tool.schemas.CoordinateType attribute) L LazyUtaDatabase (class in cool_seq_tool.sources.uta_database) LiftOver (class in cool_seq_tool.mappers.liftover) LONGEST_COMPATIBLE_REMAINING (cool_seq_tool.schemas.TranscriptPriority attribute) lower() (cool_seq_tool.resources.data_files.DataFile method) LRG_REFSEQGENE (cool_seq_tool.resources.data_files.DataFile attribute) M mane_genes (cool_seq_tool.mappers.mane_transcript.GenomicRepresentation attribute) MANE_PLUS_CLINICAL (cool_seq_tool.schemas.TranscriptPriority attribute) MANE_REFSEQ_GENOMIC (cool_seq_tool.resources.data_files.DataFile attribute) MANE_SELECT (cool_seq_tool.schemas.TranscriptPriority attribute) MANE_SUMMARY (cool_seq_tool.resources.data_files.DataFile attribute) ManeGeneData (class in cool_seq_tool.schemas) ManeStatus (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) module cool_seq_tool.app cool_seq_tool.handlers.seqrepo_access cool_seq_tool.mappers.alignment cool_seq_tool.mappers.exon_genomic_coords cool_seq_tool.mappers.feature_overlap cool_seq_tool.mappers.liftover cool_seq_tool.mappers.mane_transcript cool_seq_tool.resources.data_files 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) ncbi_gene_id (cool_seq_tool.schemas.ManeGeneData attribute) NEGATIVE (cool_seq_tool.schemas.Strand attribute) NoMatchingAlignmentError O offset (cool_seq_tool.mappers.exon_genomic_coords.TxSegment attribute) open() (cool_seq_tool.sources.uta_database.LazyUtaDatabase method) ord (cool_seq_tool.sources.uta_database.ExonCoord attribute) (cool_seq_tool.sources.uta_database.GenomicAlnData attribute) overlap (cool_seq_tool.schemas.CdsOverlap attribute) P p_to_c() (cool_seq_tool.mappers.alignment.AlignmentMapper method) p_to_c_ac() (cool_seq_tool.sources.uta_database.UtaRepository method) p_to_g() (cool_seq_tool.mappers.alignment.AlignmentMapper method) ParseResult (class in cool_seq_tool.sources.uta_database) PLUS_CLINICAL (cool_seq_tool.schemas.ManeStatus attribute) pos (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.mappers.mane_transcript.GenomicRepresentation attribute) pos_change (cool_seq_tool.schemas.GenomicTxMetadata attribute) POSITIVE (cool_seq_tool.schemas.Strand attribute) process_chromosome_input() (in module cool_seq_tool.utils) 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) repository() (cool_seq_tool.sources.uta_database.LazyUtaDatabase method) (cool_seq_tool.sources.uta_database.UtaDatabase method) RESIDUE (cool_seq_tool.schemas.CoordinateType attribute) response_datetime (cool_seq_tool.schemas.ServiceMeta attribute) S sanitized_url (cool_seq_tool.sources.uta_database.ParseResult property) schema (cool_seq_tool.sources.uta_database.ParseResult property) seg (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSeg attribute) seg_end (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService attribute) seg_start (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService attribute) SELECT (cool_seq_tool.schemas.ManeStatus attribute) SeqRepoAccess (class in cool_seq_tool.handlers.seqrepo_access) service_meta (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService attribute) service_meta() (in module cool_seq_tool.utils) ServiceMeta (class in cool_seq_tool.schemas) status (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.mappers.mane_transcript.GenomicRepresentation attribute) (cool_seq_tool.schemas.ManeGeneData attribute) Strand (class in cool_seq_tool.schemas) strand (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSeg attribute) (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService attribute) (cool_seq_tool.mappers.mane_transcript.DataRepresentation attribute) (cool_seq_tool.schemas.GenomicTxData attribute) symbol (cool_seq_tool.schemas.ManeGeneData attribute) T transcript_exists() (cool_seq_tool.sources.uta_database.UtaRepository method) TRANSCRIPT_MAPPINGS (cool_seq_tool.resources.data_files.DataFile attribute) TranscriptMappings (class in cool_seq_tool.sources.transcript_mappings) TranscriptPriority (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) tx_ac (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSeg attribute) (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService attribute) (cool_seq_tool.schemas.GenomicTxMetadata attribute) (cool_seq_tool.sources.uta_database.TxExonAlnData attribute) tx_end_i (cool_seq_tool.sources.uta_database.ExonCoord attribute) (cool_seq_tool.sources.uta_database.TxExonAlnData attribute) tx_exon_id (cool_seq_tool.schemas.GenomicTxData attribute) (cool_seq_tool.sources.uta_database.TxExonAlnData attribute) tx_pos_range (cool_seq_tool.schemas.GenomicTxData attribute) tx_segment_to_genomic() (cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper method) tx_start_i (cool_seq_tool.sources.uta_database.ExonCoord attribute) (cool_seq_tool.sources.uta_database.TxExonAlnData attribute) tx_status (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSeg attribute) (cool_seq_tool.mappers.exon_genomic_coords.GenomicTxSegService attribute) TxExonAlnData (class in cool_seq_tool.sources.uta_database) TxSegment (class in cool_seq_tool.mappers.exon_genomic_coords) U url (cool_seq_tool.schemas.ServiceMeta attribute) UtaDatabase (class in cool_seq_tool.sources.uta_database) UtaRepository (class in cool_seq_tool.sources.uta_database) V validate_genomic_ac() (cool_seq_tool.sources.uta_database.UtaRepository method) validate_genomic_breakpoint() (cool_seq_tool.sources.uta_database.UtaRepository method) validate_index() (cool_seq_tool.mappers.mane_transcript.ManeTranscript method) values() (cool_seq_tool.schemas.Assembly class method) version (cool_seq_tool.schemas.ServiceMeta attribute)