Compute intrinsic features

Computes nucleotide composition and CpG features for each target site.

Step type:: Analysis step

Run this step

ASOkai run --step compute-intrinsic-features --config-file ./config.yaml

Example configuration for this step and its dependencies:

datadir: ./data
parameters:
  genome:
    assembly: GRCh38
    release: 114
    source: ensembl
    species: Homo_sapiens
  target:
    target_id: ENSG00000133703
    k: 16
    region: pre-mrna

Parameters

These scalar configuration values are passed to this step.

Configuration path	Details
`parameters.analysis.intrinsic_features.features`	Accepted value: string; minimum string length: 1; format: ‘all’ or a comma-separated list without duplicates; choices: GC_content, AT_content, T_count, CpG_count, T_content, CpG_content; surrounding whitespace allowed Requirement: Default: all Description: Comma-separated intrinsic feature columns, or ‘all’ for every supported feature.

Parameter rules

exactly one of these config values is required: target_id, target_name

Inputs

An input with a fixed producer uses that output by default. A selected run can instead link a named output or supply an existing path. The input’s path override in config.yaml also selects an existing file. External paths are validated against the input’s file contract.

File input	Details
`target_gene`	Producer output: create-target-gene.`target_gene` Shared config source: `steps.compute-intrinsic-features.inputs.target_gene.path` or `steps.compute-intrinsic-features.inputs.target_gene.from` Format: JSON — `TargetGene` Description: Serialized target gene object from create-target-gene.

Example path-override configuration:

steps:
  compute-intrinsic-features:
    inputs:
      target_gene:
        path: /path/to/target_gene.json

Resources

Configurable resources use the first value in the resolution order shown below.

Resource setting	Details
`n_workers`	Step override: `resources.compute-intrinsic-features.n_workers` Shared default: `resources.default.n_workers` Built-in fallback: 1 Accepted value: integer; minimum: 1 Description: Number of workers allocated to a step that supports parallel execution.
`memory_mb`	Step override: `resources.compute-intrinsic-features.memory_mb` Shared default: `resources.default.memory_mb` Built-in fallback: 4096 Accepted value: integer; minimum: 1 Description: Memory in mebibytes allocated to this step.

Outputs

File output paths are relative to datadir. Braced names are replaced with the corresponding parameter values.

File outputs

File output	Details
`intrinsic_features`	Format: CSV Description: Intrinsic features per target site. Path template: `{assembly}/{source}/{release}/targets/{target}/analysis/intrinsic/{target}_k{k}_{region}_intrinsic_{features}.csv` Example path: `GRCh38/ensembl/114/targets/ENSG00000133703/analysis/intrinsic/ENSG00000133703_k16_pre-mrna_intrinsic_all.csv`

Output columns

The intrinsic_features output is the primary analysis table. It is UTF-8 and comma-separated. Its first row is a header containing exactly the columns below, in the declared order.

Rows: Intrinsic features per target site. Index columns identify the item; analysis-result columns contain the computed values.

Output column	Details
`site_id`	Role: Index Accepted value: string Meaning: Identifies the item represented by this row.
`GC_content`	Role: Analysis result Accepted value: number Meaning: The proportion of Guanine (G) and Cytosine (C) bases (between 0 and 1).
`AT_content`	Role: Analysis result Accepted value: number Meaning: The proportion of Adenine (A) and Thymine (T) bases (between 0 and 1).
`T_count`	Role: Analysis result Accepted value: integer Meaning: The count of Thymine (T) bases.
`CpG_count`	Role: Analysis result Accepted value: integer Meaning: The total count of CpG dinucleotides (a Cytosine followed by a Guanine).
`T_content`	Role: Analysis result Accepted value: number Meaning: The proportion of Thymine (T) bases (between 0 and 1).
`CpG_content`	Role: Analysis result Accepted value: number Meaning: CpG count divided by sequence length (between 0 and 1).