bulkrna-geneid-mapping

bulkrna-geneid-mapping

When to use

Convert Ensembl, Entrez and symbol identifiers in count-matrix row indexes. Use a caller-provided mapping for full coverage or non-human organisms. Skip when identifiers already match downstream needs.

Use from a step

import pandas as pd
from skills._sdk.notebook import load_skill, read_input, write_output
library = load_skill('bulkrna-geneid-mapping')
data = read_input('counts.csv', reader=lambda path: pd.read_csv(path, index_col=0))
result = library.map_ids(data)
write_output(result, 'tables/result.csv')

examples/example_step.py runs offline and supports fresh-kernel replay. Pure computations return objects; CLI and steps own writes.

API

map_ids(data, *, from_type='ensembl', to_type='symbol', species='human', on_duplicate='sum', mapping=None)

Map count-matrix row identifiers without network or file access.

:param data: Gene-by-sample counts; the row index contains source IDs. :param from_type: CLI default ensembl; entrez and symbol are also supported. :param to_type: CLI default symbol; target namespace. :param species: CLI default human; mouse requires an explicit reference. :param on_duplicate: CLI default sum; first or drop resolve target collisions differently. :param mapping: Optional source/target DataFrame; None uses ten human demo genes only. :returns: A new mapped DataFrame with reference scope, mapping records and summary diagnostics. :raises ValueError: Namespaces, duplicate policy or reference data are invalid.

fetch_mapping(data, *, from_type='ensembl', to_type='symbol', species='human')

Query MyGene explicitly and return a local source/target mapping table.

:param data: Iterable of identifiers to send to the public MyGene service. :param from_type: Default ensembl; source namespace. :param to_type: Default symbol; requested target namespace. :param species: Default human; MyGene species selector. :returns: A DataFrame containing only identifiers for which MyGene returned a match. :raises ImportError: Install mygene with install_skill_deps if unavailable. :raises Exception: Network or service errors propagate; no demo substitute is returned.