Index

Symbols

--base-uri modo-publish command line option --config modo-update command line option --element modo-add command line option --endpoint modo command line option --files modo-show command line option --force modo-remove command line option --from-file modo-add command line option modo-create command line option --meta modo-create command line option --no-remove modo-update command line option --output-format modo-publish command line option --parent modo-add command line option --query modo-search-codes command line option --region modo-stream command line option --source-file modo-add command line option --top modo-search-codes command line option

--version modo command line option --zarr modo-show command line option -c modo-update command line option -e modo-add command line option -f modo-add command line option modo-create command line option modo-remove command line option modo-show command line option -m modo-create command line option -n modo-update command line option -p modo-add command line option -q modo-search-codes command line option -r modo-stream command line option -s modo-add command line option -t modo-search-codes command line option -z modo-show command line option

_

__iter__() (modos.genomics.htsget._HtsgetBlockIter method) __next__() (modos.genomics.htsget._HtsgetBlockIter method) __post_init__() (modos.genomics.region.Region method) __version__ (in module modos) _add_any_element() (modos.api.MODO method) _blocks (modos.genomics.htsget._HtsgetBlockIter attribute) _consume_block() (modos.genomics.htsget._HtsgetBlockIter method)

_HtsgetBlockIter (class in modos.genomics.htsget) _iterator (modos.genomics.htsget.HtsgetStream attribute) _leftover (modos.genomics.htsget.HtsgetStream attribute) _path (modos.storage.LocalStorage attribute) (modos.storage.S3Storage attribute) _s3_pattern (modos.storage.S3Path attribute) _source (modos.genomics.htsget._HtsgetBlockIter attribute)

A

add_data() (in module modos.storage) add_element() (modos.api.MODO method) add_metadata_group() (in module modos.storage)

arrays (modos.io.ExtractedMetadata attribute) ASSAY (modos.helpers.schema.ElementType attribute) (modos.helpers.schema.UserElementType attribute) attrs_to_graph() (in module modos.rdf)

B

BAM (modos.genomics.formats.GenomicFileSuffix attribute) BCF (modos.genomics.formats.GenomicFileSuffix attribute)

bucket (modos.storage.S3Path property) build_htsget_url() (in module modos.genomics.htsget)

C

chrom (modos.genomics.region.Region attribute) chunk_size (modos.genomics.htsget._HtsgetBlockIter attribute) class_from_name() (in module modos.helpers.schema) Code (class in modos.codes)

CodeMatcher (class in modos.codes) connect_s3() (in module modos.storage) contains() (modos.genomics.region.Region method) CRAM (modos.genomics.formats.GenomicFileSuffix attribute) create_sequence_id() (in module modos.genomics.cram)

D

DATA_ENTITY (modos.helpers.schema.ElementType attribute) (modos.helpers.schema.UserElementType attribute)

dict_to_instance() (in module modos.helpers.schema)

E

ELEMENT_ID modo-remove command line option modo-show command line option ELEMENT_TYPE modo-add command line option elements (modos.io.ExtractedMetadata attribute) ElementType (class in modos.helpers.schema) empty() (modos.storage.Storage method) end (modos.genomics.region.Region attribute) endpoint (modos.api.MODO attribute), [1] (modos.codes.CodeMatcher attribute) (modos.codes.LocalCodeMatcher attribute) (modos.codes.RemoteCodeMatcher attribute) (modos.storage.S3Storage attribute)

EndpointManager (class in modos.remote) enrich_metadata() (modos.api.MODO method) exists() (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method) ext2loader (in module modos.io) extract_metadata() (in module modos.genomics.cram) (in module modos.io) (in module modos.metabolomics.mztab) extract_tables() (in module modos.metabolomics.mztab) ExtractedMetadata (class in modos.io)

F

FASTA (modos.genomics.formats.GenomicFileSuffix attribute) FASTQ (modos.genomics.formats.GenomicFileSuffix attribute) FILE_PATH modo-stream command line option find_codes() (modos.codes.CodeMatcher method) (modos.codes.LocalCodeMatcher method) (modos.codes.RemoteCodeMatcher method) from_file() (modos.api.MODO class method) from_htsget_query() (modos.genomics.region.Region class method)

from_model_name() (modos.helpers.schema.ElementType class method) from_object() (modos.helpers.schema.ElementType class method) (modos.helpers.schema.UserElementType class method) from_path() (modos.genomics.formats.GenomicFileSuffix class method) from_pysam() (modos.genomics.region.Region class method) from_ucsc() (modos.genomics.region.Region class method) from_url() (modos.genomics.htsget.HtsgetConnection class method) fuzon (modos.remote.EndpointManager property) fuzzy_complete() (in module modos.prompt)

G

GenomicFileSuffix (class in modos.genomics.formats) get_assay() (in module modos.metabolomics.mztab) get_completions() (modos.prompt.SlotCodeCompleter method) get_enum_values() (in module modos.helpers.schema) get_haspart_property() (in module modos.helpers.schema) get_index_suffix() (modos.genomics.formats.GenomicFileSuffix method) get_loader() (in module modos.io) get_metadata_from_remote() (in module modos.remote)

get_s3_path() (in module modos.remote) get_samples() (in module modos.metabolomics.mztab) get_slot_matcher() (in module modos.codes) get_slot_matchers() (in module modos.codes) get_slot_range() (in module modos.helpers.schema) get_slots() (in module modos.helpers.schema) get_target_class() (modos.helpers.schema.ElementType method) (modos.helpers.schema.UserElementType method)

H

host (modos.genomics.htsget.HtsgetConnection attribute) htsget (modos.remote.EndpointManager property)

HtsgetConnection (class in modos.genomics.htsget) HtsgetStream (class in modos.genomics.htsget)

I

init_zarr() (in module modos.storage) instance_to_graph() (in module modos.helpers.schema)

is_full_id() (in module modos.helpers.schema) is_s3_path() (in module modos.remote) is_uri() (in module modos.helpers.schema)

K

key (modos.storage.S3Path property)

knowledge_graph() (modos.api.MODO method)

L

label (modos.codes.Code attribute) list() (modos.remote.EndpointManager method) (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method) list_arrays() (modos.api.MODO method) list_files() (modos.api.MODO method)

list_remote_items() (in module modos.remote) list_samples() (modos.api.MODO method) list_zarr_items() (in module modos.storage) load_mztab() (in module modos.metabolomics.mztab) load_prefixmap() (in module modos.helpers.schema) load_schema() (in module modos.helpers.schema) LocalCodeMatcher (class in modos.codes) LocalStorage (class in modos.storage)

M

matcher (modos.prompt.SlotCodeCompleter attribute) metadata (modos.api.MODO property) MODO (class in modos.api) modo command line option --endpoint --version modo-add command line option --element --from-file --parent --source-file -e -f -p -s ELEMENT_TYPE OBJECT_PATH modo-create command line option --from-file --meta -f -m OBJECT_PATH modo-enrich command line option OBJECT_PATH modo-publish command line option --base-uri --output-format OBJECT_PATH modo-remove command line option --force -f ELEMENT_ID OBJECT_PATH modo-search-codes command line option --query --top -q -t SLOT modo-show command line option --files --zarr -f -z ELEMENT_ID OBJECT_PATH modo-stream command line option --region -r FILE_PATH modo-update command line option --config --no-remove -c -n OBJECT_PATH

modos module modos (modos.remote.EndpointManager attribute) modos.api module modos.codes module modos.genomics module modos.genomics.cram module modos.genomics.formats module modos.genomics.htsget module modos.genomics.region module modos.helpers module modos.helpers.schema module modos.io module modos.metabolomics module modos.metabolomics.mztab module modos.prompt module modos.rdf module modos.remote module modos.storage module module modos modos.api modos.codes modos.genomics modos.genomics.cram modos.genomics.formats modos.genomics.htsget modos.genomics.region modos.helpers modos.helpers.schema modos.io modos.metabolomics modos.metabolomics.mztab modos.prompt modos.rdf modos.remote modos.storage

O

OBJECT_PATH modo-add command line option modo-create command line option modo-enrich command line option modo-publish command line option modo-remove command line option modo-show command line option modo-update command line option

open() (modos.genomics.htsget.HtsgetConnection method) (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method) overlaps() (modos.genomics.region.Region method)

P

parse_attributes() (in module modos.io) parse_htsget_url() (in module modos.genomics.htsget) parse_instance() (in module modos.io) parse_multiple_instances() (in module modos.io) path (modos.api.MODO property) (modos.genomics.htsget.HtsgetConnection attribute) (modos.storage.LocalStorage property) (modos.storage.S3Storage property) (modos.storage.Storage property)

prompt (modos.prompt.SlotPrompter attribute) prompt_for_slot() (modos.prompt.SlotPrompter method) prompt_for_slots() (modos.prompt.SlotPrompter method) put() (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method)

Q

query() (modos.api.MODO method)

R

read_pysam() (in module modos.genomics.formats) readable() (modos.genomics.htsget.HtsgetStream method) readinto() (modos.genomics.htsget.HtsgetStream method) REFERENCE_GENOME (modos.helpers.schema.ElementType attribute) (modos.helpers.schema.UserElementType attribute) REFERENCE_SEQUENCE (modos.helpers.schema.ElementType attribute) Region (class in modos.genomics.region)

region (modos.genomics.htsget.HtsgetConnection attribute) RemoteCodeMatcher (class in modos.codes) remove() (modos.storage.LocalStorage method) (modos.storage.S3Storage method) (modos.storage.Storage method) remove_element() (modos.api.MODO method) remove_object() (modos.api.MODO method)

S

s3 (modos.remote.EndpointManager property) S3_ADDRESSING_STYLE (in module modos.storage) s3_url_parts() (modos.storage.S3Path method) S3Path (class in modos.storage) S3Storage (class in modos.storage) SAM (modos.genomics.formats.GenomicFileSuffix attribute) SAMPLE (modos.helpers.schema.ElementType attribute) (modos.helpers.schema.UserElementType attribute) SCHEMA_PATH (in module modos.helpers.schema) services (modos.remote.EndpointManager attribute) set_data_path() (in module modos.helpers.schema) set_haspart_relationship() (in module modos.helpers.schema)

show_contents() (modos.api.MODO method) SLOT modo-search-codes command line option slot (modos.codes.CodeMatcher attribute) (modos.codes.LocalCodeMatcher attribute) (modos.codes.RemoteCodeMatcher attribute) SLOT_TERMINOLOGIES (in module modos.codes) SlotCodeCompleter (class in modos.prompt) SlotPrompter (class in modos.prompt) start (modos.genomics.region.Region attribute) Storage (class in modos.storage) storage (modos.api.MODO attribute) stream_genomics() (modos.api.MODO method)

T

ticket (modos.genomics.htsget.HtsgetConnection property) timeout (modos.genomics.htsget._HtsgetBlockIter attribute) to_file() (modos.genomics.htsget.HtsgetConnection method) to_htsget_endpoint() (modos.genomics.formats.GenomicFileSuffix method) to_htsget_query() (modos.genomics.region.Region method)

to_pysam() (modos.genomics.htsget.HtsgetConnection method) to_tuple() (modos.genomics.region.Region method) top (modos.codes.CodeMatcher attribute) (modos.codes.LocalCodeMatcher attribute) (modos.codes.RemoteCodeMatcher attribute)

U

update_date() (modos.api.MODO method) update_element() (modos.api.MODO method) update_haspart_id() (in module modos.helpers.schema)

uri (modos.codes.Code attribute) url (modos.genomics.htsget.HtsgetConnection property) (modos.storage.S3Path attribute) UserElementType (class in modos.helpers.schema)

V

validate_cram_files() (in module modos.genomics.cram)

VCF (modos.genomics.formats.GenomicFileSuffix attribute)

Z

zarr (modos.api.MODO property) (modos.storage.LocalStorage property) (modos.storage.S3Storage property) (modos.storage.Storage property)

ZARR_ROOT (in module modos.storage)