Index

A

accession_to_sbol_uri() (in module scriptutils.part_retrieval)

add() (PackageInventory method)

B

build_distribution() (in module scriptutils.package_production)

BUILD_PRODUCTS_COLLECTION (in module scriptutils.package_production)

C

collate_package() (in module scriptutils.package_production)

convert_package_sbol2_files() (in module scriptutils.conversions)

D

distribution_dir() (in module scriptutils.directories) DISTRIBUTION_FASTA (in module scriptutils.directories) DISTRIBUTION_GENBANK (in module scriptutils.directories)

DISTRIBUTION_NAME (in module scriptutils.directories) DISTRIBUTION_NAMESPACE (in module scriptutils.package_specification) DISTRIBUTION_SUMMARY (in module scriptutils.generate_markdown)

E

expand_build_plan() (in module scriptutils.package_production) export_csvs() (in module scriptutils.package_specification) EXPORT_DIRECTORY (in module scriptutils.directories)

export_sbol() (in module scriptutils.package_specification) EXPORT_SHEETS (in module scriptutils.directories) extract_synthesis_files() (in module scriptutils.package_production)

F

FASTA_iGEM_PATTERN (in module scriptutils.part_retrieval)

G

generate_distribution_summary() (in module scriptutils.generate_markdown) generate_package_summary() (in module scriptutils.generate_markdown)

generic_part_download() (in module scriptutils.part_retrieval) get_sbol3_doc() (ImportFile method)

H

has_SO_uri() (in module scriptutils.helpers)

hilite() (in module scriptutils.generate_markdown)

I

id_to_uri (ImportFile attribute) IGEM_FASTA_CACHE_FILE (in module scriptutils.part_retrieval) IGEM_SBOL2_CACHE_FILE (in module scriptutils.part_retrieval) IGEM_SBOL2_TRANSIENT_CACHE_FILE (in module scriptutils.part_retrieval)

IGEM_SBOL3_CACHE_FILE (in module scriptutils.part_retrieval) iGEM_SOURCE_PREFIX (in module scriptutils.part_retrieval) import_parts() (in module scriptutils.part_retrieval) ImportFile (class in scriptutils.part_retrieval)

M

module scriptutils scriptutils.conversions scriptutils.directories scriptutils.generate_markdown scriptutils.helpers scriptutils.package_production scriptutils.package_specification scriptutils.part_retrieval

N

NCBI_GENBANK_CACHE_FILE (in module scriptutils.part_retrieval)

NCBI_PREFIX (in module scriptutils.part_retrieval)

O

OTHER_FASTA_CACHE_FILE (in module scriptutils.part_retrieval)

OTHER_GENBANK_CACHE_FILE (in module scriptutils.part_retrieval)

P

package_dirs() (in module scriptutils.directories) package_excel() (in module scriptutils.directories) package_parts_inventory() (in module scriptutils.part_retrieval)

package_stem() (in module scriptutils.package_specification) PackageInventory (class in scriptutils.part_retrieval) prefix_remappings (in module scriptutils.part_retrieval)

R

regularize_directory() (in module scriptutils.directories) remap_prefix() (in module scriptutils.part_retrieval) remove_duplicate_prefix() (in module scriptutils.helpers)

retrieve_genbank_accessions() (in module scriptutils.part_retrieval) retrieve_igem_parts() (in module scriptutils.part_retrieval) retrieve_parts() (in module scriptutils.part_retrieval) retrieve_synbiohub_parts() (in module scriptutils.part_retrieval)

S

sanitize_identifiers_for_synthesis() (in module scriptutils.helpers) SBOL_EXPORT_NAME (in module scriptutils.directories) SBOL_iGEM_PATTERNS (in module scriptutils.part_retrieval) SBOL_PACKAGE_NAME (in module scriptutils.directories) sbol_uri_to_accession() (in module scriptutils.part_retrieval) scriptutils module scriptutils.conversions module scriptutils.directories module scriptutils.generate_markdown module

scriptutils.helpers module scriptutils.package_production module scriptutils.package_specification module scriptutils.part_retrieval module SHEET_CONFIG (in module scriptutils.package_specification) source_list (in module scriptutils.part_retrieval) SUMMARY_FILE (in module scriptutils.generate_markdown)

T

truncate_by_underscores() (in module scriptutils.helpers)

V

vector_to_insert() (in module scriptutils.helpers)