BioCantor
latest
Contents:
BioCantor paradigm
Vignettes
Instantiating BioCantor objects
Location
operations
Sequence
operations
Parent
operations
Contents:
BioCantor Annotation Data Structures
Annotation Object Model
Parsing annotation files with BioCantor
Parsing GenBank files
Parsing GFF3 files
Understanding Incorporating Variation
Exporting BioCantor data models
AnnotationCollection Operations
Representing AnnotationCollections as JSON/dictionaries
Chunk-relative coordinates
Autogenerated Documentation
API Reference
BioCantor
Index
Edit on GitHub
Index
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_
_() (in module biocantor.location)
,
[1]
(in module biocantor.parent)
,
[1]
(in module biocantor.sequence)
__eq__() (biocantor.AbstractLocation method)
(biocantor.gene.codon.Codon method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
(biocantor.parent.parent.Parent method)
(biocantor.sequence.sequence.Sequence method)
__getitem__() (biocantor.sequence.sequence.Sequence method)
__getstate__() (biocantor.gene.collections.AnnotationCollection method)
__hash__() (biocantor.AbstractLocation method)
(biocantor.gene.codon.Codon method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
(biocantor.parent.parent.Parent method)
(biocantor.sequence.sequence.Sequence method)
__iter__() (biocantor.gene.interval.AbstractFeatureIntervalCollection method)
(biocantor.io.ncbi.tbl_writer.TblFeature method)
(biocantor.io.ncbi.tbl_writer.TblGene method)
__len__() (biocantor.AbstractLocation method)
(biocantor.AbstractSequence method)
(biocantor.gene.cds.CDSInterval method)
(biocantor.gene.collections.AnnotationCollection method)
(biocantor.gene.interval.AbstractFeatureInterval method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
__lt__() (biocantor.location.location_impl.SingleInterval method)
(biocantor.location.strand.Strand method)
__repr__() (biocantor.AbstractLocation method)
(biocantor.gene.cds.CDSInterval method)
(biocantor.gene.codon.Codon method)
(biocantor.gene.collections.AnnotationCollection method)
(biocantor.gene.feature.FeatureInterval method)
(biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
(biocantor.gene.variants.VariantInterval method)
(biocantor.gene.variants.VariantIntervalCollection method)
(biocantor.io.genbank.parser.GeneFeature method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
(biocantor.parent.parent.Parent method)
(biocantor.sequence.sequence.Sequence method)
__setstate__() (biocantor.gene.collections.AnnotationCollection method)
__slots__ (biocantor.AbstractLocation attribute)
(biocantor.AbstractParent attribute)
(biocantor.AbstractSequence attribute)
(biocantor.gene.codon.Codon attribute)
(biocantor.location.location.Location attribute)
(biocantor.location.location_impl.CompoundInterval attribute)
(biocantor.parent.parent.Parent attribute)
(biocantor.sequence.sequence.Sequence attribute)
__str__() (biocantor.AbstractLocation method)
(biocantor.gene.cds.CDSInterval method)
(biocantor.gene.codon.Codon method)
(biocantor.gene.feature.FeatureInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
(biocantor.gene.variants.VariantInterval method)
(biocantor.io.bed.bed.BED12 method)
(biocantor.io.bed.bed.BED3 method)
(biocantor.io.bed.bed.BED6 method)
(biocantor.io.bed.bed.RGB method)
(biocantor.io.genbank.parser.CDSFeature method)
(biocantor.io.genbank.parser.GeneFeature method)
(biocantor.io.genbank.parser.TranscriptFeature method)
(biocantor.io.gff3.rows.GFFAttributes method)
(biocantor.io.gff3.rows.GFFRow method)
(biocantor.io.ncbi.tbl_writer.TblFeature method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
(biocantor.location.strand.Strand method)
(biocantor.sequence.sequence.Sequence method)
__version__ (in module biocantor)
_associate_intervals_with_variant_intervals() (biocantor.gene.collections.AnnotationCollection method)
_build_new_collection_from_query() (biocantor.gene.collections.AnnotationCollection method)
_build_position_interval_tree() (biocantor.gene.collections.AnnotationCollection method)
_calculate_frame_offset() (biocantor.gene.cds.CDSInterval method)
_cds_interval (biocantor.io.genbank.parser.TranscriptFeature attribute)
_child_interval_guid_map (biocantor.gene.collections.AnnotationCollection property)
_chunk_relative_bounded_chromosome_location (biocantor.gene.interval.AbstractFeatureInterval property)
(biocantor.gene.interval.AbstractInterval property)
_combine_blocks() (biocantor.location.location_impl.CompoundInterval method)
_construct_gene_from_feature() (biocantor.io.genbank.parser.BaseGenBankParser static method)
_convert_chromosome_start_end_to_relative_window() (biocantor.gene.cds.CDSInterval method)
_convert_features_to_transcript() (in module biocantor.io.gff3.parser)
_convert_seqfeature_to_gene() (biocantor.io.genbank.parser.BaseGenBankParser method)
_convert_seqfeatures_to_genes() (biocantor.io.genbank.parser.BaseGenBankParser method)
_distance_to_single_interval() (biocantor.location.location_impl.SingleInterval method)
_EmptyLocation (class in biocantor.location.location_impl)
_encode_object_for_digest() (in module biocantor.util.hashing)
_escape_str() (biocantor.io.gff3.rows.GFFAttributes static method)
_escape_str_with_comma() (biocantor.io.gff3.rows.GFFAttributes static method)
_exon_interval (biocantor.io.genbank.parser.TranscriptFeature attribute)
_exon_iter() (biocantor.gene.cds.CDSInterval method)
_expand_coordinates_to_codons() (biocantor.gene.cds.CDSInterval method)
_export_annotation_collections() (biocantor.io.genbank.parser.BaseGenBankParser method)
_export_qualifiers_to_list() (biocantor.gene.interval.AbstractInterval method)
_extract_seqfeatures_from_seqrecords() (biocantor.io.genbank.parser.HybridGenBankParser method)
(biocantor.io.genbank.parser.LocusTagGenBankParser method)
(biocantor.io.genbank.parser.SortedGenBankParser method)
_find_all_top_level_non_gene_features() (in module biocantor.io.gff3.parser)
_find_non_gene_feature_types() (in module biocantor.io.gff3.parser)
_find_primary_feature() (biocantor.gene.interval.AbstractFeatureIntervalCollection static method)
_frame_iter() (biocantor.gene.cds.CDSInterval method)
_from_single_intervals_no_validation() (biocantor.location.location_impl.CompoundInterval class method)
_full_span_interval (biocantor.AbstractLocation property)
(biocantor.location.location_impl._EmptyLocation property)
(biocantor.location.location_impl.CompoundInterval property)
(biocantor.location.location_impl.SingleInterval property)
_genomic_ends (biocantor.gene.interval.AbstractFeatureInterval attribute)
_genomic_starts (biocantor.gene.interval.AbstractFeatureInterval attribute)
_GFF3ReservedQualifiers (class in biocantor.io.gff3.constants)
_group_features_by_locus_tag() (biocantor.io.genbank.parser.BaseGenBankParser method)
_group_features_by_position() (biocantor.io.genbank.parser.BaseGenBankParser method)
_group_gene_features_by_locus_tag() (biocantor.io.genbank.parser.LocusTagGenBankParser method)
_group_gene_features_by_locus_tag_and_position() (biocantor.io.genbank.parser.HybridGenBankParser method)
_group_gene_features_by_position() (biocantor.io.genbank.parser.SortedGenBankParser method)
_group_sorted_features_by_type() (biocantor.io.genbank.parser.BaseGenBankParser static method)
_has_overlap_single_interval() (biocantor.location.location_impl.SingleInterval method)
_identifiers (biocantor.gene.cds.CDSInterval attribute)
(biocantor.gene.collections.AnnotationCollection attribute)
(biocantor.gene.feature.FeatureInterval attribute)
(biocantor.gene.feature.FeatureIntervalCollection attribute)
(biocantor.gene.gene.GeneInterval attribute)
(biocantor.gene.interval.AbstractInterval attribute)
(biocantor.gene.transcript.TranscriptInterval attribute)
(biocantor.gene.variants.VariantInterval attribute)
(biocantor.gene.variants.VariantIntervalCollection attribute)
_identify_locus_tag_collisions() (biocantor.io.genbank.parser.HybridGenBankParser method)
_import_qualifiers_from_list() (biocantor.gene.interval.AbstractInterval method)
_initialize_location() (biocantor.gene.interval.AbstractFeatureIntervalCollection method)
_instance (biocantor.location.location_impl._EmptyLocation attribute)
_intersection_compound_interval() (biocantor.location.location_impl.CompoundInterval method)
_intersection_single_interval() (biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
_is_primary_feature (biocantor.gene.interval.AbstractFeatureInterval attribute)
_len (biocantor.AbstractSequence attribute)
_lift_over_chromosome_location_compound_interval() (biocantor.gene.variants.VariantInterval method)
_lift_over_chromosome_location_single_interval() (biocantor.gene.variants.VariantInterval method)
_liftover_this_location_to_seq_chunk_parent() (biocantor.gene.interval.AbstractFeatureIntervalCollection method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
_location (biocantor.gene.interval.AbstractInterval attribute)
_location_relative_to() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
_location_to_str() (biocantor.io.ncbi.tbl_writer.TblFeature method)
_merge_compound_blocks() (biocantor.location.location_impl.CompoundInterval static method)
_merge_qualifiers() (biocantor.gene.interval.AbstractFeatureInterval method)
_optimized_query_by_position() (biocantor.gene.collections.AnnotationCollection method)
_order() (biocantor.location.strand.Strand static method)
_order_dict_of_possible_sets() (in module biocantor.util.hashing)
_order_set() (in module biocantor.util.hashing)
_parent_or_seq_chunk_parent (biocantor.gene.interval.AbstractInterval attribute)
_parent_to_dict() (biocantor.gene.interval.AbstractInterval method)
_parse_child_features_to_feature_interval() (in module biocantor.io.gff3.parser)
_parse_features() (biocantor.io.genbank.parser.BaseGenBankParser method)
(in module biocantor.io.gff3.parser)
_parse_genes() (in module biocantor.io.gff3.parser)
_prepare_multi_exon_window_for_scan_codon_locations() (biocantor.gene.cds.CDSInterval method)
_prepare_single_exon_window_for_scan_codon_locations() (biocantor.gene.cds.CDSInterval method)
_produce_empty_records() (in module biocantor.io.gff3.parser)
_produce_merged_feature() (biocantor.gene.gene.GeneInterval method)
_qualifiers_to_str() (biocantor.io.ncbi.tbl_writer.TblFeature method)
_query_by_position() (biocantor.gene.collections.AnnotationCollection method)
_reset_parent() (biocantor.gene.interval.AbstractFeatureIntervalCollection method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
_return_collection_for_id_queries() (biocantor.gene.collections.AnnotationCollection method)
_scan_codon_locations() (biocantor.gene.cds.CDSInterval method)
_single_intervals (biocantor.location.location_impl.CompoundInterval property)
_singletons_ (biocantor.gene.codon.Codon attribute)
_sort_features_by_position_and_type() (biocantor.io.genbank.parser.BaseGenBankParser static method)
_sort_starts_ends() (biocantor.location.location_impl.CompoundInterval static method)
_strand (biocantor.AbstractParent attribute)
(biocantor.gene.interval.AbstractFeatureInterval attribute)
_subset_parent() (biocantor.gene.collections.AnnotationCollection method)
_to_single_interval_if_one_block() (biocantor.location.location_impl.CompoundInterval method)
_union_compound_interval() (biocantor.location.location_impl.CompoundInterval method)
_union_preserve_overlaps() (in module biocantor.location.location_impl)
_union_single_interval() (biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
_unique_value_or_none() (in module biocantor.parent.parent)
_unsorted_gff_iter() (biocantor.gene.collections.AnnotationCollection method)
_validate_alphabet() (biocantor.sequence.sequence.Sequence method)
A
AA (biocantor.sequence.alphabet.Alphabet attribute)
AA_EXTENDED (biocantor.sequence.alphabet.Alphabet attribute)
AA_EXTENDED_GAPPED (biocantor.sequence.alphabet.Alphabet attribute)
AA_STRICT_GAPPED (biocantor.sequence.alphabet.Alphabet attribute)
AA_STRICT_UNKNOWN (biocantor.sequence.alphabet.Alphabet attribute)
aacodons (in module biocantor.constants)
AbstractFeatureInterval (class in biocantor.gene.interval)
AbstractFeatureIntervalCollection (class in biocantor.gene.interval)
AbstractInterval (class in biocantor.gene.interval)
AbstractLocation (class in biocantor)
AbstractParent (class in biocantor)
AbstractSequence (class in biocantor)
add_cds_feature() (in module biocantor.io.genbank.writer)
add_child() (biocantor.io.genbank.parser.GeneFeature method)
ALIAS (biocantor.io.gff3.constants._GFF3ReservedQualifiers attribute)
alphabet (biocantor.AbstractSequence attribute)
(biocantor.io.models.ParentModel attribute)
(biocantor.io.parser.ParsedAnnotationRecord attribute)
Alphabet (class in biocantor.sequence.alphabet)
(in module biocantor)
ALPHABET_TO_NUCLEOTIDE_COMPLEMENT (in module biocantor.sequence.alphabet)
AlphabetError
alternative_genomic_sequence (biocantor.gene.variants.VariantInterval property)
(biocantor.gene.variants.VariantIntervalCollection property)
annotation (biocantor.io.parser.ParsedAnnotationRecord attribute)
AnnotationCollection (class in biocantor.gene.collections)
AnnotationCollectionModel (class in biocantor.io.models)
append() (biocantor.sequence.sequence.Sequence method)
assert_directional() (biocantor.location.strand.Strand method)
ATTRIBUTE_SEPARATOR (in module biocantor.io.gff3.constants)
attributes (biocantor.io.gff3.rows.GFFRow attribute)
B
b (biocantor.io.bed.bed.RGB attribute)
BaseGenBankParser (class in biocantor.io.genbank.parser)
BaseModel (class in biocantor.io.models)
BaseModel.Meta (class in biocantor.io.models)
BED12 (class in biocantor.io.bed.bed)
BED3 (class in biocantor.io.bed.bed)
BED6 (class in biocantor.io.bed.bed)
BEDExportException
BEDMissingSequenceNameError
bin (biocantor.gene.interval.AbstractInterval attribute)
bins() (in module biocantor.util.bins)
biocantor
module
biocantor.constants
module
biocantor.exc
module
biocantor.gene
module
biocantor.gene.biotype
module
biocantor.gene.cds
module
biocantor.gene.cds_frame
module
biocantor.gene.codon
module
biocantor.gene.collections
module
biocantor.gene.feature
module
biocantor.gene.gene
module
biocantor.gene.interval
module
biocantor.gene.transcript
module
biocantor.gene.variants
module
biocantor.io
module
biocantor.io.bed
module
biocantor.io.bed.bed
module
biocantor.io.bed.exc
module
biocantor.io.exc
module
biocantor.io.fasta
module
biocantor.io.fasta.exc
module
biocantor.io.fasta.fasta
module
biocantor.io.features
module
biocantor.io.genbank
module
biocantor.io.genbank.constants
module
biocantor.io.genbank.exc
module
biocantor.io.genbank.parser
module
biocantor.io.genbank.writer
module
biocantor.io.gff3
module
biocantor.io.gff3.constants
module
biocantor.io.gff3.exc
module
biocantor.io.gff3.parser
module
biocantor.io.gff3.rows
module
biocantor.io.gff3.writer
module
biocantor.io.models
module
biocantor.io.ncbi
module
biocantor.io.ncbi.exc
module
biocantor.io.ncbi.tbl_writer
module
biocantor.io.parser
module
biocantor.io.vcf
module
biocantor.io.vcf.parser
module
biocantor.location
module
biocantor.location.location
module
biocantor.location.location_impl
module
biocantor.location.strand
module
biocantor.parent
module
biocantor.parent.parent
module
biocantor.sequence
module
biocantor.sequence.alphabet
module
biocantor.sequence.sequence
module
biocantor.util
module
biocantor.util.bins
module
biocantor.util.enum
module
biocantor.util.hashing
module
biocantor.util.object_validation
module
biocantor.util.ordering
module
biocantor.util.types
module
BIOCANTOR_QUALIFIERS_REGEX (in module biocantor.io.gff3.constants)
BioCantorException
BioCantorFeatureTypes (class in biocantor.io.gff3.constants)
BioCantorGFF3ReservedQualifiers (class in biocantor.io.gff3.constants)
BioCantorIOException
BioCantorQualifiers (class in biocantor.io.gff3.constants)
Biotype (in module biocantor.gene.biotype)
block_count (biocantor.io.bed.bed.BED12 attribute)
block_sizes (biocantor.io.bed.bed.BED12 attribute)
block_starts (biocantor.io.bed.bed.BED12 attribute)
blocks (biocantor.AbstractLocation property)
(biocantor.gene.interval.AbstractFeatureInterval property)
(biocantor.gene.interval.AbstractInterval property)
(biocantor.location.location_impl._EmptyLocation property)
(biocantor.location.location_impl.CompoundInterval property)
(biocantor.location.location_impl.SingleInterval property)
C
CDS (biocantor.io.genbank.constants.GeneIntervalFeatures attribute)
(biocantor.io.gff3.constants.BioCantorFeatureTypes attribute)
(biocantor.io.gff3.constants.GFF3GeneFeatureTypes attribute)
cds_blocks (biocantor.gene.transcript.TranscriptInterval property)
cds_chunk_relative_location (biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
cds_end (biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
cds_ends (biocantor.io.models.TranscriptIntervalModel attribute)
cds_features (biocantor.io.genbank.parser.GroupedGeneFeatures attribute)
cds_frames (biocantor.io.models.TranscriptIntervalModel attribute)
cds_interval_to_chunk_relative() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
cds_interval_to_sequence() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
cds_location (biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
cds_pos_to_chunk_relative() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
cds_pos_to_sequence() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
cds_pos_to_transcript() (biocantor.gene.transcript.TranscriptInterval method)
cds_size (biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
cds_start (biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
cds_starts (biocantor.io.models.TranscriptIntervalModel attribute)
CDSFeature (class in biocantor.io.genbank.parser)
CDSFrame (class in biocantor.gene.cds_frame)
CDSInterval (class in biocantor.gene.cds)
CDSPhase (class in biocantor.gene.cds_frame)
CDSTblFeature (class in biocantor.io.ncbi.tbl_writer)
chars_to_remove (biocantor.io.ncbi.tbl_writer.TblFeature attribute)
children (biocantor.gene.collections.AnnotationCollection property)
(biocantor.io.ncbi.tbl_writer.TblFeature attribute)
children_guids (biocantor.gene.collections.AnnotationCollection property)
(biocantor.gene.feature.FeatureIntervalCollection property)
(biocantor.gene.gene.GeneInterval property)
(biocantor.gene.variants.VariantIntervalCollection property)
children_guids() (biocantor.gene.interval.AbstractFeatureIntervalCollection method)
chrom (biocantor.io.bed.bed.BED3 attribute)
CHROMOSOME (biocantor.SequenceType attribute)
chromosome_codon_locations (biocantor.gene.cds.CDSInterval property)
chromosome_gaps_location (biocantor.gene.interval.AbstractFeatureInterval property)
chromosome_intron_location (biocantor.gene.transcript.TranscriptInterval property)
chromosome_location (biocantor.gene.interval.AbstractFeatureInterval property)
(biocantor.gene.interval.AbstractInterval property)
chromosome_span (biocantor.gene.interval.AbstractFeatureInterval property)
chunk_relative_blocks (biocantor.gene.interval.AbstractInterval property)
chunk_relative_cds_blocks (biocantor.gene.transcript.TranscriptInterval property)
chunk_relative_cds_end (biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
chunk_relative_cds_size (biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
chunk_relative_cds_start (biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
chunk_relative_codon_locations (biocantor.gene.cds.CDSInterval property)
chunk_relative_end (biocantor.gene.interval.AbstractInterval property)
chunk_relative_frames (biocantor.gene.cds.CDSInterval property)
chunk_relative_gaps_location (biocantor.gene.interval.AbstractFeatureInterval property)
chunk_relative_interval_to_cds() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
chunk_relative_interval_to_feature() (biocantor.gene.interval.AbstractFeatureInterval method)
chunk_relative_interval_to_transcript() (biocantor.gene.transcript.TranscriptInterval method)
chunk_relative_intron_location (biocantor.gene.transcript.TranscriptInterval property)
chunk_relative_location (biocantor.gene.interval.AbstractInterval property)
chunk_relative_pos_to_cds() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
chunk_relative_pos_to_feature() (biocantor.gene.interval.AbstractFeatureInterval method)
chunk_relative_pos_to_transcript() (biocantor.gene.transcript.TranscriptInterval method)
chunk_relative_size (biocantor.gene.interval.AbstractInterval property)
chunk_relative_span (biocantor.gene.interval.AbstractFeatureInterval property)
chunk_relative_start (biocantor.gene.interval.AbstractInterval property)
chunk_relative_strand (biocantor.gene.interval.AbstractInterval property)
CODING_TRANSCRIPT (biocantor.io.genbank.constants.TranscriptFeatures attribute)
Codon (class in biocantor.gene.codon)
CODON_START (biocantor.io.genbank.constants.KnownQualifiers attribute)
collection_to_fasta() (in module biocantor.io.fasta.fasta)
collection_to_genbank() (in module biocantor.io.genbank.writer)
collection_to_gff3() (in module biocantor.io.gff3.writer)
collection_to_tbl() (in module biocantor.io.ncbi.tbl_writer)
compare() (biocantor.location.location_impl.SingleInterval method)
completely_within (biocantor.io.models.AnnotationCollectionModel attribute)
CompoundInterval (class in biocantor.location.location_impl)
construct_frames() (biocantor.io.genbank.parser.TranscriptFeature method)
construct_frames_from_location() (biocantor.gene.cds.CDSInterval static method)
contains() (biocantor.AbstractLocation method)
(biocantor.location.location.Location method)
convert_vcf_records_to_model() (in module biocantor.io.vcf.parser)
COORD_OFFSETS (in module biocantor.util.bins)
D
DBXREF (biocantor.io.genbank.constants.KnownQualifiers attribute)
(biocantor.io.gff3.constants._GFF3ReservedQualifiers attribute)
DEFAULT (biocantor.gene.codon.TranslationTable attribute)
default_parse_func() (in module biocantor.io.gff3.parser)
DERIVES_FROM (biocantor.io.gff3.constants._GFF3ReservedQualifiers attribute)
digest_object() (in module biocantor.util.hashing)
distance_to() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
DistanceType (class in biocantor)
DuplicateFeatureError
DuplicateFeatureWarning
DuplicateSequenceException
DuplicateTranscriptError
DuplicateTranscriptWarning
E
EmptyGenBankError
EmptyGFF3Exception
EmptyLocation() (in module biocantor.location.location_impl)
EmptyLocationException
EmptySequenceFastaError
ENCODING_MAP (in module biocantor.io.gff3.constants)
ENCODING_MAP_WITH_COMMA (in module biocantor.io.gff3.constants)
ENCODING_PATTERN (in module biocantor.io.gff3.constants)
ENCODING_PATTERN_WITH_COMMA (in module biocantor.io.gff3.constants)
end (biocantor.AbstractLocation attribute)
(biocantor.gene.interval.AbstractInterval attribute)
(biocantor.io.bed.bed.BED3 attribute)
(biocantor.io.gff3.rows.GFFRow attribute)
(biocantor.io.models.AnnotationCollectionModel attribute)
(biocantor.io.models.ParentModel attribute)
(biocantor.io.models.VariantIntervalModel attribute)
(biocantor.location.location_impl._EmptyLocation property)
ENDS (biocantor.DistanceType attribute)
equals_except_location() (biocantor.AbstractParent method)
(biocantor.parent.parent.Parent method)
escape_key() (biocantor.io.gff3.rows.GFFAttributes static method)
escape_value() (biocantor.io.gff3.rows.GFFAttributes static method)
EUKARYOTIC (biocantor.io.genbank.constants.GenbankFlavor attribute)
EXON (biocantor.io.genbank.constants.GeneIntervalFeatures attribute)
(biocantor.io.gff3.constants.BioCantorFeatureTypes attribute)
(biocantor.io.gff3.constants.GFF3GeneFeatureTypes attribute)
exon_ends (biocantor.io.models.TranscriptIntervalModel attribute)
exon_starts (biocantor.io.models.TranscriptIntervalModel attribute)
export_qualifiers() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.feature.FeatureInterval method)
(biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
(biocantor.gene.interval.AbstractFeatureInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
(biocantor.gene.variants.VariantInterval method)
extend_absolute() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
extend_relative() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
extended_gencode (in module biocantor.constants)
extract_dbxref_synonyms() (biocantor.io.ncbi.tbl_writer.TblFeature static method)
extract_feature_name_id() (in module biocantor.io.features)
extract_feature_types() (in module biocantor.io.features)
extract_seqrecords_from_gff3_fasta() (in module biocantor.io.gff3.parser)
extract_sequence() (biocantor.AbstractLocation method)
(biocantor.gene.cds.CDSInterval method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
F
FASTA_HEADER (biocantor.io.gff3.constants.GFF3Headers attribute)
fasta_to_parents() (in module biocantor.io.fasta.fasta)
FastaExportError
FEATURE (biocantor.gene.interval.IntervalType attribute)
Feature (class in biocantor.io.genbank.parser)
FEATURE_CLASS (biocantor.io.genbank.constants.KnownQualifiers attribute)
FEATURE_COLLECTION (biocantor.io.genbank.constants.FeatureCollectionFeatures attribute)
(biocantor.io.gff3.constants.BioCantorFeatureTypes attribute)
feature_collection_guid (biocantor.io.models.FeatureIntervalCollectionModel attribute)
FEATURE_COLLECTION_ID (biocantor.io.gff3.constants.BioCantorQualifiers attribute)
feature_collection_id (biocantor.io.models.FeatureIntervalCollectionModel attribute)
FEATURE_COLLECTION_NAME (biocantor.io.gff3.constants.BioCantorQualifiers attribute)
feature_collection_name (biocantor.io.models.FeatureIntervalCollectionModel attribute)
feature_collection_type (biocantor.io.models.FeatureIntervalCollectionModel attribute)
feature_collections (biocantor.io.models.AnnotationCollectionModel attribute)
FEATURE_COLLETION_TYPE (biocantor.io.gff3.constants.BioCantorQualifiers attribute)
feature_guid (biocantor.io.models.FeatureIntervalModel attribute)
FEATURE_ID (biocantor.io.features.FeatureIntervalIDQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorQualifiers attribute)
feature_id (biocantor.io.models.FeatureIntervalModel attribute)
FEATURE_INTERVAL (biocantor.io.genbank.constants.FeatureIntervalFeatures attribute)
(biocantor.io.gff3.constants.BioCantorFeatureTypes attribute)
feature_interval_guid (biocantor.io.models.FeatureIntervalModel attribute)
FEATURE_INTERVAL_ID_QUALIFIERS (in module biocantor.io.features)
FEATURE_INTERVAL_ID_QUALIFIERS_REGEX (in module biocantor.io.features)
FEATURE_INTERVAL_NAME_QUALIFIERS (in module biocantor.io.features)
FEATURE_INTERVAL_NAME_QUALIFIERS_REGEX (in module biocantor.io.features)
FEATURE_INTERVAL_REGION (biocantor.io.gff3.constants.BioCantorFeatureTypes attribute)
feature_interval_to_chunk_relative() (biocantor.gene.interval.AbstractFeatureInterval method)
feature_interval_to_sequence() (biocantor.gene.interval.AbstractFeatureInterval method)
feature_intervals (biocantor.io.models.FeatureIntervalCollectionModel attribute)
feature_intervals_to_features() (in module biocantor.io.genbank.writer)
FEATURE_NAME (biocantor.io.features.FeatureIntervalNameQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorQualifiers attribute)
feature_name (biocantor.io.models.FeatureIntervalModel attribute)
feature_pos_to_chunk_relative() (biocantor.gene.interval.AbstractFeatureInterval method)
feature_pos_to_sequence() (biocantor.gene.interval.AbstractFeatureInterval method)
FEATURE_SYMBOL (biocantor.io.gff3.constants.BioCantorQualifiers attribute)
FEATURE_TYPE (biocantor.io.gff3.constants.BioCantorQualifiers attribute)
(biocantor.io.ncbi.tbl_writer.CDSTblFeature attribute)
(biocantor.io.ncbi.tbl_writer.GeneTblFeature attribute)
(biocantor.io.ncbi.tbl_writer.MiscRNATblFeature attribute)
(biocantor.io.ncbi.tbl_writer.MRNATblFeature attribute)
(biocantor.io.ncbi.tbl_writer.NcRNATblFeature attribute)
(biocantor.io.ncbi.tbl_writer.RRNATblFeature attribute)
(biocantor.io.ncbi.tbl_writer.TblFeature attribute)
(biocantor.io.ncbi.tbl_writer.TRNATblFeature attribute)
FEATURE_TYPE_IDENTIFIERS (in module biocantor.io.features)
FEATURE_TYPE_IDENTIFIERS_REGEX (in module biocantor.io.features)
feature_types (biocantor.io.models.FeatureIntervalModel attribute)
FeatureCollectionFeatures (class in biocantor.io.genbank.constants)
FeatureInterval (class in biocantor.gene.feature)
FeatureIntervalCollection (class in biocantor.gene.feature)
FeatureIntervalCollectionModel (class in biocantor.io.models)
FeatureIntervalFeatures (class in biocantor.io.genbank.constants)
FeatureIntervalGenBankCollection (class in biocantor.io.genbank.parser)
FeatureIntervalIDQualifiers (class in biocantor.io.features)
FeatureIntervalModel (class in biocantor.io.models)
FeatureIntervalNameQualifiers (class in biocantor.io.features)
filter_and_sort_qualifiers() (in module biocantor.io.gff3.parser)
find_cds_interval() (biocantor.io.genbank.parser.TranscriptFeature method)
find_exon_interval() (biocantor.io.genbank.parser.TranscriptFeature method)
find_transcript_interval() (biocantor.io.genbank.parser.TranscriptFeature method)
first_ancestor_of_type() (biocantor.AbstractLocation method)
(biocantor.AbstractParent method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.location.location.Location method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.parent.parent.Parent method)
(biocantor.sequence.sequence.Sequence method)
FIRST_SHIFT (in module biocantor.util.bins)
frames (biocantor.gene.cds.CDSInterval attribute)
from_annotation_collection() (biocantor.io.models.AnnotationCollectionModel static method)
from_chunk_relative_location() (biocantor.gene.cds.CDSInterval static method)
(biocantor.gene.feature.FeatureInterval static method)
(biocantor.gene.transcript.TranscriptInterval static method)
from_dict() (biocantor.gene.cds.CDSInterval static method)
(biocantor.gene.collections.AnnotationCollection static method)
(biocantor.gene.feature.FeatureInterval static method)
(biocantor.gene.feature.FeatureIntervalCollection static method)
(biocantor.gene.gene.GeneInterval static method)
(biocantor.gene.interval.AbstractInterval static method)
(biocantor.gene.transcript.TranscriptInterval static method)
(biocantor.gene.variants.VariantInterval static method)
(biocantor.gene.variants.VariantIntervalCollection static method)
from_feature_collection() (biocantor.io.models.FeatureIntervalCollectionModel static method)
from_feature_interval() (biocantor.io.models.FeatureIntervalModel static method)
from_gene_interval() (biocantor.io.models.GeneIntervalModel static method)
from_int() (biocantor.gene.cds_frame.CDSFrame static method)
(biocantor.gene.cds_frame.CDSPhase static method)
(biocantor.location.strand.Strand static method)
from_location() (biocantor.gene.cds.CDSInterval static method)
(biocantor.gene.feature.FeatureInterval static method)
(biocantor.gene.transcript.TranscriptInterval static method)
from_single_intervals() (biocantor.location.location_impl.CompoundInterval class method)
from_symbol() (biocantor.location.strand.Strand static method)
from_transcript_interval() (biocantor.io.models.TranscriptIntervalModel static method)
from_transcript_or_cds_feature() (biocantor.io.genbank.parser.GeneFeature static method)
from_variant_interval() (biocantor.io.models.VariantIntervalModel static method)
from_variant_interval_collection() (biocantor.io.models.VariantIntervalCollectionModel static method)
G
g (biocantor.io.bed.bed.RGB attribute)
GAP (biocantor.io.gff3.constants._GFF3ReservedQualifiers attribute)
gap_list() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
gaps_location() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
GBKEY (biocantor.io.genbank.constants.KnownQualifiers attribute)
GENBANK_GENE_FEATURES (in module biocantor.io.genbank.constants)
genbank_parser_type (biocantor.io.genbank.parser.BaseGenBankParser attribute)
(biocantor.io.genbank.parser.HybridGenBankParser attribute)
(biocantor.io.genbank.parser.LocusTagGenBankParser attribute)
(biocantor.io.genbank.parser.SortedGenBankParser attribute)
GenBankDuplicateLocusTagWarning
GenBankEmptyGeneWarning
GenBankExportError
GenbankFlavor (class in biocantor.io.genbank.constants)
GenBankLocationException
GenBankLocusTagError
GenBankMultipleTranscriptFeatureError
GenBankNullStrandException
GenBankParserError
GenBankParserType (class in biocantor.io.genbank.constants)
GenBankUnknownFeatureWarning
gencode (in module biocantor.constants)
GENE (biocantor.io.features.FeatureIntervalNameQualifiers attribute)
(biocantor.io.genbank.constants.GeneFeatures attribute)
(biocantor.io.genbank.constants.KnownQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorFeatureTypes attribute)
(biocantor.io.gff3.constants.GFF3GeneFeatureTypes attribute)
gene_feature (biocantor.io.genbank.parser.GroupedGeneFeatures attribute)
gene_guid (biocantor.io.models.GeneIntervalModel attribute)
GENE_ID (biocantor.io.genbank.constants.KnownQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorQualifiers attribute)
gene_id (biocantor.io.models.GeneIntervalModel attribute)
GENE_NAME (biocantor.io.features.FeatureIntervalNameQualifiers attribute)
(biocantor.io.genbank.constants.KnownQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorQualifiers attribute)
GENE_SYMBOL (biocantor.io.gff3.constants.BioCantorQualifiers attribute)
gene_symbol (biocantor.io.models.GeneIntervalModel attribute)
GENE_SYNONYM (biocantor.io.genbank.constants.KnownQualifiers attribute)
gene_to_feature() (in module biocantor.io.genbank.writer)
GENE_TYPE (biocantor.io.gff3.constants.BioCantorQualifiers attribute)
gene_type (biocantor.io.models.GeneIntervalModel attribute)
GeneFeature (class in biocantor.io.genbank.parser)
GeneFeatures (class in biocantor.io.genbank.constants)
GeneInterval (class in biocantor.gene.gene)
GeneIntervalFeatures (class in biocantor.io.genbank.constants)
GeneIntervalModel (class in biocantor.io.models)
GENERIC (biocantor.sequence.alphabet.Alphabet attribute)
genes (biocantor.io.models.AnnotationCollectionModel attribute)
GeneTblFeature (class in biocantor.io.ncbi.tbl_writer)
get_3p_interval() (biocantor.gene.transcript.TranscriptInterval method)
get_5p_interval() (biocantor.gene.transcript.TranscriptInterval method)
get_cds_sequence() (biocantor.gene.transcript.TranscriptInterval method)
get_children_by_type() (biocantor.gene.collections.AnnotationCollection method)
get_genomic_sequence() (biocantor.gene.interval.AbstractFeatureInterval method)
get_merged_cds() (biocantor.gene.gene.GeneInterval method)
get_merged_feature() (biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
get_merged_transcript() (biocantor.gene.gene.GeneInterval method)
get_primary_cds() (biocantor.gene.gene.GeneInterval method)
get_primary_cds_sequence() (biocantor.gene.gene.GeneInterval method)
get_primary_feature() (biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
get_primary_feature_sequence() (biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
get_primary_protein() (biocantor.gene.gene.GeneInterval method)
get_primary_transcript() (biocantor.gene.gene.GeneInterval method)
get_primary_transcript_sequence() (biocantor.gene.gene.GeneInterval method)
get_protein_sequence() (biocantor.gene.transcript.TranscriptInterval method)
get_qualifier_from_tx_or_cds_features() (biocantor.io.genbank.parser.TranscriptFeature method)
get_reference_sequence() (biocantor.gene.interval.AbstractFeatureInterval method)
(biocantor.gene.interval.AbstractFeatureIntervalCollection method)
get_spliced_sequence() (biocantor.gene.interval.AbstractFeatureInterval method)
get_transcript_sequence() (biocantor.gene.transcript.TranscriptInterval method)
GFF3ChildParentMismatchError
GFF3ExportException
GFF3FastaException
GFF3GeneFeatureTypes (class in biocantor.io.gff3.constants)
GFF3Headers (class in biocantor.io.gff3.constants)
GFF3LocusTagError
GFF3MissingSequenceNameError
GFF3ParserError
GFF3ReservedQualifiers (in module biocantor.io.gff3.constants)
GFF_SOURCE (in module biocantor.io.gff3.constants)
GFFAttributes (class in biocantor.io.gff3.rows)
GFFRow (class in biocantor.io.gff3.rows)
GffutilsParseArgs (class in biocantor.io.gff3.parser)
GREATER (biocantor.util.ordering.RelativeOrder attribute)
GroupedGeneFeatures (class in biocantor.io.genbank.parser)
guid (biocantor.gene.interval.AbstractInterval attribute)
H
has_ancestor_of_type() (biocantor.AbstractLocation method)
(biocantor.AbstractParent method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.location.location.Location method)
(biocantor.parent.parent.Parent method)
(biocantor.sequence.sequence.Sequence method)
has_ancestor_sequence() (biocantor.AbstractLocation method)
(biocantor.AbstractParent method)
(biocantor.location.location.Location method)
(biocantor.parent.parent.Parent method)
has_canonical_start_codon (biocantor.gene.cds.CDSInterval property)
HAS_CGRANGES (in module biocantor.gene.collections)
(in module biocantor.location.location_impl)
has_children (biocantor.io.genbank.parser.GeneFeature property)
has_in_frame_stop (biocantor.gene.cds.CDSInterval property)
(biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
has_name() (biocantor.util.enum.HasMemberMixin class method)
has_overlap() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
has_sequence (biocantor.gene.interval.AbstractInterval property)
has_start_codon_in_specific_translation_table() (biocantor.gene.cds.CDSInterval method)
has_valid_stop (biocantor.gene.cds.CDSInterval property)
has_value() (biocantor.util.enum.HasMemberMixin class method)
HasMemberMixin (class in biocantor.util.enum)
HEADER (biocantor.io.gff3.constants.GFF3Headers attribute)
hierarchical_children_guids (biocantor.gene.collections.AnnotationCollection property)
HYBRID (biocantor.io.genbank.constants.GenBankParserType attribute)
HybridGenBankParser (class in biocantor.io.genbank.parser)
I
id (biocantor.AbstractParent attribute)
(biocantor.AbstractSequence attribute)
(biocantor.gene.cds.CDSInterval property)
(biocantor.gene.collections.AnnotationCollection property)
(biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.feature.FeatureIntervalCollection property)
(biocantor.gene.gene.GeneInterval property)
(biocantor.gene.interval.AbstractInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
(biocantor.gene.variants.VariantInterval property)
(biocantor.gene.variants.VariantIntervalCollection property)
ID (biocantor.io.features.FeatureIntervalIDQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorGFF3ReservedQualifiers attribute)
id (biocantor.io.models.AnnotationCollectionModel attribute)
id_spec (biocantor.io.gff3.parser.GffutilsParseArgs attribute)
identifiers (biocantor.gene.interval.AbstractInterval property)
identifiers_dict (biocantor.gene.interval.AbstractInterval property)
incorporate_variants() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.collections.AnnotationCollection method)
(biocantor.gene.feature.FeatureInterval method)
(biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
infer_child() (biocantor.io.genbank.parser.GeneFeature method)
initialize_location() (biocantor.gene.interval.AbstractInterval static method)
INNER (biocantor.DistanceType attribute)
intersect() (biocantor.gene.feature.FeatureInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
intersection() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
interval_ends (biocantor.io.models.FeatureIntervalModel attribute)
interval_guids_to_collections (biocantor.gene.collections.AnnotationCollection property)
interval_starts (biocantor.io.models.FeatureIntervalModel attribute)
interval_type (biocantor.gene.feature.FeatureInterval attribute)
(biocantor.gene.feature.FeatureIntervalCollection attribute)
(biocantor.gene.gene.GeneInterval attribute)
(biocantor.gene.transcript.TranscriptInterval attribute)
(biocantor.gene.variants.VariantIntervalCollection attribute)
IntervalType (class in biocantor.gene.interval)
InvalidAnnotationError
InvalidCDSIntervalError
InvalidCDSIntervalWarning
InvalidInputError
InvalidIntervalWarning
InvalidPositionException
InvalidQueryError
InvalidStrandException
is_canonical_start_codon (biocantor.gene.codon.Codon property)
is_chunk_relative (biocantor.gene.interval.AbstractInterval property)
is_coding (biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.feature.FeatureIntervalCollection property)
(biocantor.gene.gene.GeneInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
is_contiguous (biocantor.AbstractLocation property)
(biocantor.location.location_impl._EmptyLocation property)
(biocantor.location.location_impl.CompoundInterval property)
(biocantor.location.location_impl.SingleInterval property)
is_empty (biocantor.AbstractLocation property)
(biocantor.gene.collections.AnnotationCollection property)
(biocantor.location.location_impl._EmptyLocation property)
(biocantor.location.location_impl.CompoundInterval property)
(biocantor.location.location_impl.SingleInterval property)
(biocantor.sequence.sequence.Sequence property)
is_nucleotide_alphabet() (biocantor.sequence.alphabet.Alphabet method)
is_overlapping (biocantor.AbstractLocation property)
(biocantor.location.location_impl._EmptyLocation property)
(biocantor.location.location_impl.CompoundInterval property)
(biocantor.location.location_impl.SingleInterval property)
is_primary_feature (biocantor.gene.interval.AbstractFeatureInterval property)
(biocantor.io.models.FeatureIntervalModel attribute)
is_primary_tx (biocantor.gene.transcript.TranscriptInterval property)
(biocantor.io.models.TranscriptIntervalModel attribute)
is_start_codon_in_specific_translation_table() (biocantor.gene.codon.Codon method)
is_stop_codon (biocantor.gene.codon.Codon property)
is_strict_codon (biocantor.gene.codon.Codon property)
item_rgb (biocantor.io.bed.bed.BED12 attribute)
iter_children() (biocantor.gene.collections.AnnotationCollection method)
(biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
(biocantor.gene.interval.AbstractFeatureIntervalCollection method)
(biocantor.gene.variants.VariantIntervalCollection method)
(biocantor.io.ncbi.tbl_writer.TblFeature method)
iter_non_variant_children() (biocantor.gene.collections.AnnotationCollection method)
K
KnownQualifiers (class in biocantor.io.genbank.constants)
L
LABEL (biocantor.io.features.FeatureIntervalNameQualifiers attribute)
length (biocantor.AbstractLocation attribute)
(biocantor.location.location_impl._EmptyLocation property)
length_difference (biocantor.gene.variants.VariantInterval property)
LESS (biocantor.util.ordering.RelativeOrder attribute)
lift_child_location_to_parent() (biocantor.AbstractParent method)
(biocantor.parent.parent.Parent method)
lift_over_location() (biocantor.gene.variants.VariantInterval method)
(biocantor.gene.variants.VariantIntervalCollection method)
lift_over_to_first_ancestor_of_type() (biocantor.AbstractLocation method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.location.location.Location method)
lift_over_to_sequence() (biocantor.AbstractLocation method)
(biocantor.location.location.Location method)
liftover_location_to_seq_chunk_parent() (biocantor.gene.interval.AbstractInterval static method)
liftover_to_parent_or_seq_chunk_parent() (biocantor.gene.interval.AbstractInterval method)
location (biocantor.AbstractParent attribute)
Location (class in biocantor.location.location)
(in module biocantor.sequence.sequence)
location_on_parent (biocantor.sequence.sequence.Sequence property)
location_relative_to() (biocantor.AbstractLocation method)
(biocantor.location.location.Location method)
(biocantor.location.location_impl._EmptyLocation method)
LocationException
LocationOverlapException
LOCUS_TAG (biocantor.io.genbank.constants.GenBankParserType attribute)
(biocantor.io.genbank.constants.KnownQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorQualifiers attribute)
locus_tag (biocantor.io.models.FeatureIntervalCollectionModel attribute)
(biocantor.io.models.GeneIntervalModel attribute)
LocusTagException
LocusTagGenBankParser (class in biocantor.io.genbank.parser)
logger (in module biocantor.io.gff3.parser)
M
make_parent() (in module biocantor.parent)
MAX_CHROM_SIZE (in module biocantor.util.bins)
merge_cds_qualifiers_to_transcript() (biocantor.io.genbank.parser.TranscriptFeature method)
merge_overlapping() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
merge_qualifiers() (in module biocantor.io.features)
merge_strategy (biocantor.io.gff3.parser.GffutilsParseArgs attribute)
MetadataFeatures (class in biocantor.io.genbank.constants)
MINUS (biocantor.location.strand.Strand attribute)
minus() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
MISC_RNA (biocantor.io.genbank.constants.NonCodingTranscriptFeatures attribute)
(biocantor.io.genbank.constants.TranscriptFeatures attribute)
MiscRNATblFeature (class in biocantor.io.ncbi.tbl_writer)
MismatchedFrameException
MismatchedParentException
module
biocantor
biocantor.constants
biocantor.exc
biocantor.gene
biocantor.gene.biotype
biocantor.gene.cds
biocantor.gene.cds_frame
biocantor.gene.codon
biocantor.gene.collections
biocantor.gene.feature
biocantor.gene.gene
biocantor.gene.interval
biocantor.gene.transcript
biocantor.gene.variants
biocantor.io
biocantor.io.bed
biocantor.io.bed.bed
biocantor.io.bed.exc
biocantor.io.exc
biocantor.io.fasta
biocantor.io.fasta.exc
biocantor.io.fasta.fasta
biocantor.io.features
biocantor.io.genbank
biocantor.io.genbank.constants
biocantor.io.genbank.exc
biocantor.io.genbank.parser
biocantor.io.genbank.writer
biocantor.io.gff3
biocantor.io.gff3.constants
biocantor.io.gff3.exc
biocantor.io.gff3.parser
biocantor.io.gff3.rows
biocantor.io.gff3.writer
biocantor.io.models
biocantor.io.ncbi
biocantor.io.ncbi.exc
biocantor.io.ncbi.tbl_writer
biocantor.io.parser
biocantor.io.vcf
biocantor.io.vcf.parser
biocantor.location
biocantor.location.location
biocantor.location.location_impl
biocantor.location.strand
biocantor.parent
biocantor.parent.parent
biocantor.sequence
biocantor.sequence.alphabet
biocantor.sequence.sequence
biocantor.util
biocantor.util.bins
biocantor.util.enum
biocantor.util.hashing
biocantor.util.object_validation
biocantor.util.ordering
biocantor.util.types
MRNATblFeature (class in biocantor.io.ncbi.tbl_writer)
N
name (biocantor.gene.cds.CDSInterval property)
(biocantor.gene.codon.Codon property)
(biocantor.gene.collections.AnnotationCollection property)
(biocantor.gene.feature.FeatureInterval property)
(biocantor.gene.feature.FeatureIntervalCollection property)
(biocantor.gene.gene.GeneInterval property)
(biocantor.gene.interval.AbstractInterval property)
(biocantor.gene.transcript.TranscriptInterval property)
(biocantor.gene.variants.VariantInterval property)
(biocantor.gene.variants.VariantIntervalCollection property)
(biocantor.io.bed.bed.BED6 attribute)
NAME (biocantor.io.features.FeatureIntervalNameQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorGFF3ReservedQualifiers attribute)
name (biocantor.io.models.AnnotationCollectionModel attribute)
NcRNATblFeature (class in biocantor.io.ncbi.tbl_writer)
NEITHER (biocantor.util.ordering.RelativeOrder attribute)
NEXT_SHIFT (in module biocantor.util.bins)
non_variant_children (biocantor.gene.collections.AnnotationCollection property)
NONCODING_TRANSCRIPT (biocantor.io.genbank.constants.NonCodingTranscriptFeatures attribute)
(biocantor.io.genbank.constants.TranscriptFeatures attribute)
NoncodingTranscriptError
NonCodingTranscriptFeatures (class in biocantor.io.genbank.constants)
NONE (biocantor.gene.cds_frame.CDSFrame attribute)
(biocantor.gene.cds_frame.CDSPhase attribute)
NoSuchAncestorException
NOTE (biocantor.io.gff3.constants._GFF3ReservedQualifiers attribute)
NT_EXTENDED (biocantor.sequence.alphabet.Alphabet attribute)
NT_EXTENDED_GAPPED (biocantor.sequence.alphabet.Alphabet attribute)
NT_STRICT (biocantor.sequence.alphabet.Alphabet attribute)
NT_STRICT_GAPPED (biocantor.sequence.alphabet.Alphabet attribute)
NT_STRICT_UNKNOWN (biocantor.sequence.alphabet.Alphabet attribute)
NULL_COLUMN (in module biocantor.io.gff3.constants)
NullParentException
NullSequenceException
num_blocks (biocantor.AbstractLocation property)
(biocantor.gene.interval.AbstractInterval property)
(biocantor.location.location_impl._EmptyLocation property)
(biocantor.location.location_impl.CompoundInterval property)
(biocantor.location.location_impl.SingleInterval property)
num_chunk_relative_blocks (biocantor.gene.interval.AbstractInterval property)
num_chunk_relative_codons (biocantor.gene.cds.CDSInterval property)
num_codons (biocantor.gene.cds.CDSInterval property)
num_feature_collections (biocantor.io.genbank.parser.BaseGenBankParser property)
num_genes (biocantor.io.genbank.parser.BaseGenBankParser property)
O
ObjectValidation (class in biocantor.util.object_validation)
OFFSETS (in module biocantor.util.bins)
ONE (biocantor.gene.cds_frame.CDSFrame attribute)
(biocantor.gene.cds_frame.CDSPhase attribute)
ONTOLOGY_TERM (biocantor.io.gff3.constants._GFF3ReservedQualifiers attribute)
OPERON (biocantor.io.features.FeatureIntervalNameQualifiers attribute)
optimize_and_combine_blocks() (biocantor.gene.cds.CDSInterval method)
(biocantor.location.location_impl.CompoundInterval method)
optimize_blocks() (biocantor.AbstractLocation method)
(biocantor.gene.cds.CDSInterval method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
ordered (biocantor.io.models.BaseModel.Meta attribute)
OUTER (biocantor.DistanceType attribute)
P
parent (biocantor.AbstractLocation attribute)
(biocantor.AbstractParent attribute)
(biocantor.AbstractSequence attribute)
PARENT (biocantor.io.gff3.constants.BioCantorGFF3ReservedQualifiers attribute)
parent (biocantor.location.location_impl._EmptyLocation property)
Parent (class in biocantor.parent.parent)
(in module biocantor.parent.parent)
PARENT_CACHE_SIZE (in module biocantor.parent.parent)
parent_id (biocantor.AbstractLocation property)
(biocantor.sequence.sequence.Sequence property)
parent_or_seq_chunk_parent (biocantor.io.models.AnnotationCollectionModel attribute)
parent_strand (biocantor.sequence.sequence.Sequence property)
parent_to_relative_location() (biocantor.AbstractLocation method)
(biocantor.location.location.Location method)
(biocantor.location.location_impl._EmptyLocation method)
parent_to_relative_pos() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
parent_type (biocantor.AbstractLocation property)
(biocantor.sequence.sequence.Sequence property)
parent_with_alternative_sequence (biocantor.gene.variants.VariantInterval property)
(biocantor.gene.variants.VariantIntervalCollection property)
ParentException
ParentInputType (in module biocantor.parent.parent)
(in module biocantor.sequence.sequence)
(in module biocantor.util.types)
ParentModel (class in biocantor.io.models)
parse() (biocantor.io.genbank.parser.BaseGenBankParser method)
(biocantor.io.genbank.parser.HybridGenBankParser method)
(biocantor.io.genbank.parser.LocusTagGenBankParser method)
(biocantor.io.genbank.parser.SortedGenBankParser method)
parse_genbank() (in module biocantor.io.genbank.parser)
parse_gff3_embedded_fasta() (in module biocantor.io.gff3.parser)
parse_gff3_fasta() (in module biocantor.io.gff3.parser)
parse_standard_gff3() (in module biocantor.io.gff3.parser)
parse_vcf_file() (in module biocantor.io.vcf.parser)
parsed_annotation_records_to_model() (biocantor.io.parser.ParsedAnnotationRecord static method)
ParsedAnnotationRecord (class in biocantor.io.parser)
phase (biocantor.io.gff3.rows.GFFRow attribute)
phase_block (biocantor.io.models.VariantIntervalModel attribute)
PLUS (biocantor.location.strand.Strand attribute)
post_dump() (biocantor.io.models.AnnotationCollectionModel method)
PRODUCT (biocantor.io.genbank.constants.KnownQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorQualifiers attribute)
product (biocantor.io.models.TranscriptIntervalModel attribute)
PROKARYOTE (biocantor.gene.codon.TranslationTable attribute)
PROKARYOTIC (biocantor.io.genbank.constants.GenbankFlavor attribute)
PROTEIN_ID (biocantor.io.genbank.constants.KnownQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorQualifiers attribute)
protein_id (biocantor.io.models.TranscriptIntervalModel attribute)
PSEUDOGENE (biocantor.io.gff3.constants.GFF3GeneFeatureTypes attribute)
Q
qualifiers (biocantor.gene.interval.AbstractInterval attribute)
(biocantor.io.models.AnnotationCollectionModel attribute)
(biocantor.io.models.FeatureIntervalCollectionModel attribute)
(biocantor.io.models.FeatureIntervalModel attribute)
(biocantor.io.models.GeneIntervalModel attribute)
(biocantor.io.models.TranscriptIntervalModel attribute)
(biocantor.io.models.VariantIntervalCollectionModel attribute)
(biocantor.io.models.VariantIntervalModel attribute)
QualifierValue (in module biocantor.gene.interval)
query_by_feature_identifiers() (biocantor.gene.collections.AnnotationCollection method)
query_by_feature_interval_guids() (biocantor.gene.collections.AnnotationCollection method)
query_by_guids() (biocantor.gene.collections.AnnotationCollection method)
(biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
(biocantor.gene.interval.AbstractFeatureIntervalCollection method)
(biocantor.gene.variants.VariantIntervalCollection method)
query_by_interval_guids() (biocantor.gene.collections.AnnotationCollection method)
query_by_position() (biocantor.gene.collections.AnnotationCollection method)
query_by_transcript_interval_guids() (biocantor.gene.collections.AnnotationCollection method)
R
r (biocantor.io.bed.bed.RGB attribute)
random_uppercase_str() (in module biocantor.io.ncbi.tbl_writer)
relative_blocks (biocantor.gene.interval.AbstractFeatureInterval property)
relative_interval_to_parent_location() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
relative_to() (biocantor.location.strand.Strand method)
relative_to_parent_pos() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
RelativeOrder (class in biocantor.util.ordering)
require_location_has_parent() (biocantor.util.object_validation.ObjectValidation static method)
require_location_has_parent_with_sequence() (biocantor.util.object_validation.ObjectValidation static method)
require_location_nonempty() (biocantor.util.object_validation.ObjectValidation static method)
require_locations_do_not_overlap() (biocantor.util.object_validation.ObjectValidation static method)
require_locations_have_same_nonempty_parent() (biocantor.util.object_validation.ObjectValidation static method)
require_locations_overlap() (biocantor.util.object_validation.ObjectValidation static method)
require_object_has_type() (biocantor.util.object_validation.ObjectValidation static method)
require_parent_has_location() (biocantor.util.object_validation.ObjectValidation static method)
require_parent_has_parent() (biocantor.util.object_validation.ObjectValidation static method)
require_parent_has_parent_with_location() (biocantor.util.object_validation.ObjectValidation static method)
require_parents_equal_except_location() (biocantor.util.object_validation.ObjectValidation static method)
require_parents_equal_except_location_and_sequence() (biocantor.util.object_validation.ObjectValidation static method)
ReservedKeyWarning
reset_location() (biocantor.AbstractParent method)
(biocantor.parent.parent.Parent method)
reset_parent() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
reset_strand() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
reverse() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
(biocantor.location.strand.Strand method)
reverse_complement() (biocantor.sequence.sequence.Sequence method)
reverse_strand() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
RGB (class in biocantor.io.bed.bed)
RIBOSOMAL_RNA (biocantor.io.genbank.constants.NonCodingTranscriptFeatures attribute)
(biocantor.io.genbank.constants.TranscriptFeatures attribute)
RRNATblFeature (class in biocantor.io.ncbi.tbl_writer)
S
scan_blocks() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
scan_chromosome_codon_locations() (biocantor.gene.cds.CDSInterval method)
scan_chunk_relative_codon_locations() (biocantor.gene.cds.CDSInterval method)
scan_codon_locations() (biocantor.gene.cds.CDSInterval method)
scan_codons() (biocantor.gene.cds.CDSInterval method)
scan_windows() (biocantor.AbstractLocation method)
(biocantor.location.location.Location method)
Schema (biocantor.io.models.BaseModel attribute)
score (biocantor.io.bed.bed.BED6 attribute)
(biocantor.io.gff3.rows.GFFRow attribute)
seq (biocantor.io.models.ParentModel attribute)
seq_chunk_to_parent() (in module biocantor.io.parser)
seq_to_parent() (in module biocantor.io.parser)
seqid (biocantor.io.gff3.rows.GFFRow attribute)
seqrecord (biocantor.io.genbank.parser.GroupedGeneFeatures attribute)
(biocantor.io.parser.ParsedAnnotationRecord attribute)
sequence (biocantor.AbstractParent attribute)
(biocantor.AbstractSequence attribute)
(biocantor.io.models.VariantIntervalModel attribute)
Sequence (class in biocantor.sequence.sequence)
(in module biocantor.sequence.sequence)
SEQUENCE_CHUNK (biocantor.SequenceType attribute)
sequence_guid (biocantor.gene.interval.AbstractInterval attribute)
(biocantor.io.models.AnnotationCollectionModel attribute)
(biocantor.io.models.FeatureIntervalCollectionModel attribute)
(biocantor.io.models.FeatureIntervalModel attribute)
(biocantor.io.models.GeneIntervalModel attribute)
(biocantor.io.models.TranscriptIntervalModel attribute)
(biocantor.io.models.VariantIntervalCollectionModel attribute)
SEQUENCE_HEADER (biocantor.io.gff3.constants.GFF3Headers attribute)
sequence_interval_to_cds() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
sequence_interval_to_feature() (biocantor.gene.interval.AbstractFeatureInterval method)
sequence_interval_to_transcript() (biocantor.gene.transcript.TranscriptInterval method)
sequence_name (biocantor.gene.interval.AbstractInterval attribute)
(biocantor.io.models.AnnotationCollectionModel attribute)
(biocantor.io.models.FeatureIntervalCollectionModel attribute)
(biocantor.io.models.FeatureIntervalModel attribute)
(biocantor.io.models.GeneIntervalModel attribute)
(biocantor.io.models.ParentModel attribute)
(biocantor.io.models.TranscriptIntervalModel attribute)
(biocantor.io.models.VariantIntervalCollectionModel attribute)
sequence_path (biocantor.io.models.AnnotationCollectionModel attribute)
sequence_pos_to_amino_acid() (biocantor.gene.cds.CDSInterval method)
sequence_pos_to_cds() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
sequence_pos_to_feature() (biocantor.gene.interval.AbstractFeatureInterval method)
sequence_pos_to_transcript() (biocantor.gene.transcript.TranscriptInterval method)
sequence_type (biocantor.AbstractParent attribute)
(biocantor.AbstractSequence attribute)
sequence_type_str_to_type() (biocantor.SequenceType static method)
SequenceType (class in biocantor)
shift() (biocantor.gene.cds_frame.CDSFrame method)
shift_position() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
SingleInterval (class in biocantor.location.location_impl)
SORTED (biocantor.io.genbank.constants.GenBankParserType attribute)
SortedGenBankParser (class in biocantor.io.genbank.parser)
SOURCE (biocantor.io.genbank.constants.MetadataFeatures attribute)
source (biocantor.io.gff3.rows.GFFRow attribute)
STANDARD (biocantor.gene.codon.TranslationTable attribute)
STANDARD_NAME (biocantor.io.features.FeatureIntervalNameQualifiers attribute)
start (biocantor.AbstractLocation attribute)
(biocantor.gene.interval.AbstractInterval attribute)
(biocantor.io.bed.bed.BED3 attribute)
(biocantor.io.genbank.parser.Feature property)
(biocantor.io.genbank.parser.FeatureIntervalGenBankCollection property)
(biocantor.io.gff3.rows.GFFRow attribute)
(biocantor.io.models.AnnotationCollectionModel attribute)
(biocantor.io.models.ParentModel attribute)
(biocantor.io.models.VariantIntervalModel attribute)
(biocantor.location.location_impl._EmptyLocation property)
START_CODONS_BY_TRANSLATION_TABLE (in module biocantor.gene.codon)
STARTS (biocantor.DistanceType attribute)
strand (biocantor.AbstractLocation attribute)
(biocantor.AbstractParent property)
(biocantor.gene.interval.AbstractFeatureIntervalCollection property)
(biocantor.gene.interval.AbstractInterval property)
(biocantor.io.bed.bed.BED6 attribute)
(biocantor.io.genbank.parser.Feature property)
(biocantor.io.gff3.rows.GFFRow attribute)
(biocantor.io.models.FeatureIntervalModel attribute)
(biocantor.io.models.ParentModel attribute)
(biocantor.io.models.TranscriptIntervalModel attribute)
(biocantor.location.location_impl._EmptyLocation property)
(biocantor.parent.parent.Parent property)
Strand (class in biocantor.location.strand)
(in module biocantor)
StrandViolationWarning
strip_location_info() (biocantor.AbstractParent method)
(biocantor.parent.parent.Parent method)
summary() (biocantor.sequence.sequence.Sequence method)
synonymous_codons() (biocantor.gene.codon.Codon method)
T
TARGET (biocantor.io.gff3.constants._GFF3ReservedQualifiers attribute)
TblExportException
TblFeature (class in biocantor.io.ncbi.tbl_writer)
TblGene (class in biocantor.io.ncbi.tbl_writer)
thick_end (biocantor.io.bed.bed.BED12 attribute)
thick_start (biocantor.io.bed.bed.BED12 attribute)
TM_RNA (biocantor.io.genbank.constants.NonCodingTranscriptFeatures attribute)
(biocantor.io.genbank.constants.TranscriptFeatures attribute)
to_annotation_collection() (biocantor.io.models.AnnotationCollectionModel method)
(biocantor.io.parser.ParsedAnnotationRecord method)
to_bed12() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.feature.FeatureInterval method)
(biocantor.gene.interval.AbstractFeatureInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
(biocantor.gene.variants.VariantInterval method)
to_biopython() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
to_compound_location() (biocantor.location.location_impl.CompoundInterval method)
to_dict() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.collections.AnnotationCollection method)
(biocantor.gene.feature.FeatureInterval method)
(biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
(biocantor.gene.variants.VariantInterval method)
(biocantor.gene.variants.VariantIntervalCollection method)
to_fasta() (biocantor.io.parser.ParsedAnnotationRecord method)
(biocantor.sequence.sequence.Sequence method)
to_feature_collection() (biocantor.io.models.FeatureIntervalCollectionModel method)
to_feature_interval() (biocantor.io.models.FeatureIntervalModel method)
to_feature_location() (biocantor.location.location_impl.SingleInterval method)
to_feature_model() (biocantor.io.genbank.parser.FeatureIntervalGenBankCollection static method)
to_frame() (biocantor.gene.cds_frame.CDSPhase method)
to_gene_interval() (biocantor.io.models.GeneIntervalModel method)
to_gene_model() (biocantor.io.genbank.parser.GeneFeature static method)
to_gff() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.cds_frame.CDSPhase method)
(biocantor.gene.collections.AnnotationCollection method)
(biocantor.gene.feature.FeatureInterval method)
(biocantor.gene.feature.FeatureIntervalCollection method)
(biocantor.gene.gene.GeneInterval method)
(biocantor.gene.interval.AbstractFeatureInterval method)
(biocantor.gene.interval.AbstractInterval method)
(biocantor.gene.transcript.TranscriptInterval method)
(biocantor.gene.variants.VariantInterval method)
(biocantor.gene.variants.VariantIntervalCollection method)
to_parent() (biocantor.io.models.ParentModel method)
to_phase() (biocantor.gene.cds_frame.CDSFrame method)
to_symbol() (biocantor.location.strand.Strand method)
to_transcript_interval() (biocantor.io.models.TranscriptIntervalModel method)
to_variant_interval() (biocantor.io.models.VariantIntervalModel method)
to_variant_interval_collection() (biocantor.io.models.VariantIntervalCollectionModel method)
to_vcf() (biocantor.gene.variants.VariantInterval method)
TRANSCRIPT (biocantor.gene.interval.IntervalType attribute)
(biocantor.io.gff3.constants.BioCantorFeatureTypes attribute)
(biocantor.io.gff3.constants.GFF3GeneFeatureTypes attribute)
transcript_features (biocantor.io.genbank.parser.GroupedGeneFeatures attribute)
transcript_guid (biocantor.io.models.TranscriptIntervalModel attribute)
TRANSCRIPT_ID (biocantor.io.genbank.constants.KnownQualifiers attribute)
(biocantor.io.gff3.constants.BioCantorQualifiers attribute)
transcript_id (biocantor.io.models.TranscriptIntervalModel attribute)
transcript_interval_guid (biocantor.io.models.TranscriptIntervalModel attribute)
transcript_interval_to_chunk_relative() (biocantor.gene.transcript.TranscriptInterval method)
transcript_interval_to_sequence() (biocantor.gene.transcript.TranscriptInterval method)
TRANSCRIPT_NAME (biocantor.io.gff3.constants.BioCantorQualifiers attribute)
transcript_pos_to_cds() (biocantor.gene.transcript.TranscriptInterval method)
transcript_pos_to_chunk_relative() (biocantor.gene.transcript.TranscriptInterval method)
transcript_pos_to_sequence() (biocantor.gene.transcript.TranscriptInterval method)
transcript_symbol (biocantor.io.models.TranscriptIntervalModel attribute)
TRANSCRIPT_TYPE (biocantor.io.gff3.constants.BioCantorQualifiers attribute)
transcript_type (biocantor.io.models.TranscriptIntervalModel attribute)
TranscriptFeature (class in biocantor.io.genbank.parser)
TranscriptFeatures (class in biocantor.io.genbank.constants)
TranscriptInterval (class in biocantor.gene.transcript)
TranscriptIntervalModel (class in biocantor.io.models)
transcripts (biocantor.io.models.GeneIntervalModel attribute)
transcripts_to_feature() (in module biocantor.io.genbank.writer)
TRANSFER_RNA (biocantor.io.genbank.constants.NonCodingTranscriptFeatures attribute)
(biocantor.io.genbank.constants.TranscriptFeatures attribute)
translate() (biocantor.gene.cds.CDSInterval method)
(biocantor.gene.codon.Codon method)
TranslationTable (class in biocantor.gene.codon)
TRNATblFeature (class in biocantor.io.ncbi.tbl_writer)
TWO (biocantor.gene.cds_frame.CDSFrame attribute)
(biocantor.gene.cds_frame.CDSPhase attribute)
type (biocantor.io.genbank.parser.Feature property)
(biocantor.io.genbank.parser.GeneFeature property)
(biocantor.io.gff3.rows.GFFRow attribute)
(biocantor.io.models.ParentModel attribute)
types (biocantor.io.genbank.parser.CDSFeature attribute)
(biocantor.io.genbank.parser.Feature attribute)
(biocantor.io.genbank.parser.GeneFeature attribute)
(biocantor.io.genbank.parser.TranscriptFeature attribute)
U
union() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
union_preserve_overlaps() (biocantor.AbstractLocation method)
(biocantor.location.location_impl._EmptyLocation method)
(biocantor.location.location_impl.CompoundInterval method)
(biocantor.location.location_impl.SingleInterval method)
UNKNOWN_BIOTYPE (in module biocantor.gene.biotype)
UnknownGenBankFeatureWarning
UNSTRANDED (biocantor.location.strand.Strand attribute)
UnsupportedOperationException
V
VALID_KEYS (biocantor.io.ncbi.tbl_writer.CDSTblFeature attribute)
(biocantor.io.ncbi.tbl_writer.GeneTblFeature attribute)
(biocantor.io.ncbi.tbl_writer.MiscRNATblFeature attribute)
(biocantor.io.ncbi.tbl_writer.MRNATblFeature attribute)
(biocantor.io.ncbi.tbl_writer.NcRNATblFeature attribute)
(biocantor.io.ncbi.tbl_writer.RRNATblFeature attribute)
(biocantor.io.ncbi.tbl_writer.TblFeature attribute)
(biocantor.io.ncbi.tbl_writer.TRNATblFeature attribute)
validate_alphabet() (biocantor.sequence.sequence.Sequence static method)
validate_seqfeature() (biocantor.io.genbank.parser.BaseGenBankParser static method)
ValidationException
value (biocantor.gene.codon.Codon property)
VARIANT (biocantor.gene.interval.IntervalType attribute)
variant_collection_guid (biocantor.io.models.VariantIntervalCollectionModel attribute)
variant_collection_id (biocantor.io.models.VariantIntervalCollectionModel attribute)
variant_collection_name (biocantor.io.models.VariantIntervalCollectionModel attribute)
variant_collections (biocantor.io.models.AnnotationCollectionModel attribute)
variant_guid (biocantor.io.models.VariantIntervalModel attribute)
variant_id (biocantor.io.models.VariantIntervalModel attribute)
variant_interval_guid (biocantor.io.models.VariantIntervalModel attribute)
variant_intervals (biocantor.io.models.VariantIntervalCollectionModel attribute)
variant_name (biocantor.io.models.VariantIntervalModel attribute)
variant_type (biocantor.io.models.VariantIntervalModel attribute)
VariantInterval (class in biocantor.gene.variants)
VariantIntervalCollection (class in biocantor.gene.variants)
VariantIntervalCollectionModel (class in biocantor.io.models)
VariantIntervalModel (class in biocantor.io.models)
Z
ZERO (biocantor.gene.cds_frame.CDSFrame attribute)
(biocantor.gene.cds_frame.CDSPhase attribute)
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