mecfs_bio.build_system.task.protein_coloc.protein_accessions_reader

Source-specific readers turning a proteomics source's protein table into the UniProt accessions of each measured protein: one row per distinct (protein id, UniProt accession).

A protein complex (for example EBI3_IL27) gives one row per subunit accession.

Classes:

• ProteinAccessionsReader –
• St3ProteinAccessionsReader –

  UKB-PPP: the extracted Sun et al. 2023 ST3 sheet, keyed by Olink id.

Attributes:

• PROTEIN_ACCESSIONS_PROTEIN_ID_COL –
• PROTEIN_ACCESSIONS_SCHEMA –
• PROTEIN_ACCESSIONS_UNIPROT_COL –

PROTEIN_ACCESSIONS_PROTEIN_ID_COL module-attribute

PROTEIN_ACCESSIONS_PROTEIN_ID_COL = 'protein_id'

PROTEIN_ACCESSIONS_SCHEMA module-attribute

PROTEIN_ACCESSIONS_SCHEMA = pl.Schema(
    {
        PROTEIN_ACCESSIONS_PROTEIN_ID_COL: pl.String,
        PROTEIN_ACCESSIONS_UNIPROT_COL: pl.String,
    }
)

PROTEIN_ACCESSIONS_UNIPROT_COL module-attribute

PROTEIN_ACCESSIONS_UNIPROT_COL = 'uniprot_id'

ProteinAccessionsReader

Bases: Protocol

St3ProteinAccessionsReader

UKB-PPP: the extracted Sun et al. 2023 ST3 sheet, keyed by Olink id.