Index

A

add_relation() (gffbase.interface.FeatureDB method) add_relations() (gffbase.interface.FeatureDB method) all_features() (gffbase.interface.FeatureDB method) analyze() (gffbase.interface.FeatureDB method) annotate_gff_db() (in module gffbase.helpers) applied (gffbase.migrate.MigrationResult attribute)

asinterval() (in module gffbase.helpers) astuple() (gffbase.feature.Feature method) attribute_checked (gffbase.validate.ValidationReport attribute) attribute_eligible (gffbase.validate.ValidationReport attribute) attribute_search() (gffbase.interface.FeatureDB method) attributes (gffbase.feature.Feature attribute) AttributeStringError

B

bed12() (gffbase.interface.FeatureDB method)

bin (gffbase.feature.Feature attribute) bins() (in module gffbase.bins)

C

calc_bin() (gffbase.feature.Feature method) canonical_transcripts() (in module gffbase.helpers) changed (gffbase.migrate.MigrationResult attribute) checked (gffbase.validate.ValidationReport attribute) checked_ids (gffbase.validate.ValidationReport attribute) children (gffbase.feature.Feature attribute) children() (gffbase.interface.FeatureDB method) children_batched() (gffbase.interface.FeatureDB method) children_bp() (gffbase.interface.FeatureDB method) chrom (gffbase.feature.Feature property) close() (gffbase.gffwriter.GFFWriter method) (gffbase.interface.FeatureDB method)

closed (gffbase.interface.FeatureDB property) ClosedDatabaseError coalesce_multipart() (in module gffbase.migrate) COORD_OFFSETS (in module gffbase.bins) count (gffbase.validate.Violation attribute) count_features_of_type() (gffbase.interface.FeatureDB method) covered_length (gffbase.feature.MultipartFeature property) create_db() (in module gffbase.create_db) create_introns() (gffbase.interface.FeatureDB method) create_splice_sites() (gffbase.interface.FeatureDB method)

D

DataIterator (class in gffbase.iterators) delete() (gffbase.interface.FeatureDB method) derived_source (gffbase.interface.FeatureDB property) detail (gffbase.validate.Violation attribute) detect_dialect() (in module gffbase.parser)

dialect (gffbase.feature.Feature attribute) (gffbase.ingest.IngestStats attribute) dialect_compare() (in module gffbase.helpers) directives (gffbase.ingest.IngestStats attribute) DuplicateIDError

E

EmptyInputError end (gffbase.feature.Feature attribute) errors (gffbase.validate.ValidationReport property) exact_coordinates_only() (in module gffbase.merge_criteria)

example_filename() (in module gffbase.helpers) examples (gffbase.validate.Violation attribute) execute() (gffbase.interface.FeatureDB method) export_sqlite() (in module gffbase.sqlite_export) extra (gffbase.feature.Feature attribute)

F

Feature (class in gffbase.feature) feature_type() (in module gffbase.merge_criteria) FeatureDB (class in gffbase.interface) FeatureNotFoundError features_of_type() (gffbase.interface.FeatureDB method) FeatureSegment (class in gffbase.feature) featuretype (gffbase.feature.Feature attribute)

featuretypes() (gffbase.interface.FeatureDB method) file_order (gffbase.feature.Feature attribute) FIRST_SHIFT (in module gffbase.bins) fmt (gffbase.ingest.IngestStats attribute) frame (gffbase.feature.Feature attribute) from_file() (in module gffbase.ingest) from_version (gffbase.migrate.MigrationResult attribute)

G

get_gff_db() (in module gffbase.helpers) gffbase.bins module gffbase.convert module gffbase.exceptions module gffbase.helpers module

gffbase.inspect module gffbase.merge_criteria module gffbase.migrate module gffbase.validate module GFFFormatError GFFWriter (class in gffbase.gffwriter)

H

HERE (in module gffbase.helpers)

I

id (gffbase.feature.Feature attribute) infer_dialect() (in module gffbase.helpers) IngestStats (class in gffbase.ingest) inspect() (in module gffbase.inspect) interfeatures() (gffbase.interface.FeatureDB method)

invariant (gffbase.validate.Violation attribute) is_gff_db() (in module gffbase.helpers) is_multipart (gffbase.feature.Feature attribute) (gffbase.feature.MultipartFeature attribute) iter_by_parent_childs() (gffbase.interface.FeatureDB method)

K

keep_order (gffbase.feature.Feature attribute)

L

level (gffbase.validate.ValidationReport attribute)

LEVELS (in module gffbase.validate)

M

make_query() (in module gffbase.helpers) merge() (gffbase.interface.FeatureDB method) merge_all() (gffbase.interface.FeatureDB method) merge_attributes() (in module gffbase.helpers) method() (gffbase.interface.FeatureDB method) migrate_v1_to_v2() (in module gffbase.migrate) MigrationResult (class in gffbase.migrate) module gffbase.bins gffbase.convert gffbase.exceptions gffbase.helpers gffbase.inspect gffbase.merge_criteria gffbase.migrate gffbase.validate

MultipartConstraintError MultipartFeature (class in gffbase.feature)

N

n_attributes (gffbase.ingest.IngestStats attribute) n_closure_rows (gffbase.ingest.IngestStats attribute) n_edges (gffbase.ingest.IngestStats attribute) n_features_raw (gffbase.ingest.IngestStats attribute) n_features_synthetic_genes (gffbase.ingest.IngestStats attribute) n_features_synthetic_transcripts (gffbase.ingest.IngestStats attribute)

n_multipart (gffbase.ingest.IngestStats attribute) n_segments (gffbase.feature.Feature attribute) (gffbase.feature.MultipartFeature attribute) n_skipped (gffbase.ingest.IngestStats attribute) name (gffbase.validate.Violation attribute) native_available() (in module gffbase.parser) NEXT_SHIFT (in module gffbase.bins)

O

OFFSETS (in module gffbase.bins) ok (gffbase.validate.ValidationReport property) overlap_any_inclusive() (in module gffbase.merge_criteria) overlap_any_threshold() (in module gffbase.merge_criteria)

overlap_end_inclusive() (in module gffbase.merge_criteria) overlap_end_threshold() (in module gffbase.merge_criteria) overlap_start_inclusive() (in module gffbase.merge_criteria) overlap_start_threshold() (in module gffbase.merge_criteria)

P

parents() (gffbase.interface.FeatureDB method) parents_batched() (gffbase.interface.FeatureDB method)

parse_bytes() (in module gffbase.parser) parse_gff() (in module gffbase.parser) print_bin_sizes() (in module gffbase.bins)

R

raise_for_status() (gffbase.validate.ValidationReport method) read_only (gffbase.interface.FeatureDB property) ReadOnlyError

region() (gffbase.interface.FeatureDB method) region_batched() (gffbase.interface.FeatureDB method) rtree_built (gffbase.ingest.IngestStats attribute)

S

sanitize_gff_db() (in module gffbase.helpers) sanitize_gff_file() (in module gffbase.helpers) schema() (gffbase.interface.FeatureDB method) SchemaVersionError score (gffbase.feature.Feature attribute) seg_idx (gffbase.feature.FeatureSegment attribute) segments (gffbase.feature.Feature property) (gffbase.feature.MultipartFeature property) seqid (gffbase.feature.Feature attribute) seqid() (in module gffbase.merge_criteria) seqids() (gffbase.interface.FeatureDB method)

sequence() (gffbase.feature.Feature method) set_pragmas() (gffbase.interface.FeatureDB method) severity (gffbase.validate.Violation attribute) skipped (gffbase.validate.ValidationReport attribute) sort_attribute_values (gffbase.feature.Feature attribute) source (gffbase.feature.Feature attribute) start (gffbase.feature.Feature attribute) stop (gffbase.feature.Feature property) strand (gffbase.feature.Feature attribute) strand() (in module gffbase.merge_criteria) SynthesisConflictError

T

to_bed12() (in module gffbase.convert) to_line() (gffbase.feature.Feature method) to_lines() (gffbase.feature.Feature method) (gffbase.feature.MultipartFeature method)

to_table() (gffbase.interface.FeatureDB method) to_unicode() (in module gffbase.helpers) to_version (gffbase.migrate.MigrationResult attribute)

U

update() (gffbase.interface.FeatureDB method)

V

validate() (gffbase.interface.FeatureDB method) validate_db() (in module gffbase.validate) ValidationError

ValidationReport (class in gffbase.validate) Violation (class in gffbase.validate) violations (gffbase.validate.ValidationReport attribute)

W

warnings (gffbase.ingest.IngestStats attribute) (gffbase.interface.FeatureDB attribute) (gffbase.validate.ValidationReport property) write_exon_children() (gffbase.gffwriter.GFFWriter method)

write_gene_recs() (gffbase.gffwriter.GFFWriter method) write_mRNA_children() (gffbase.gffwriter.GFFWriter method) write_rec() (gffbase.gffwriter.GFFWriter method) write_recs() (gffbase.gffwriter.GFFWriter method)