Create target gene

Creates a target gene, extracts target sites, and writes a region FASTA.

Step type:: Core step

Run this step

ASOkai run --step create-target-gene --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.target.target_id`	Accepted value: string or null; minimum string length: 1 Requirement: Exactly one of target_id, target_name is required when parameters.target is configured Description: Ensembl gene ID; use this or target_name, but not both.
`parameters.target.target_name`	Accepted value: string or null; minimum string length: 1 Requirement: Exactly one of target_id, target_name is required when parameters.target is configured Description: Gene name; use this or target_id, but not both.
`parameters.target.k`	Accepted value: integer; minimum: 1 Requirement: Required Description: Target-site length.
`parameters.target.region`	Accepted value: string; one of: exonic, pre-mrna, transcriptomic Requirement: Required Description: Target region type.
`parameters.genome.assembly`	Accepted value: string; minimum string length: 1 Requirement: Required Description: Genome assembly ID, such as GRCh38.
`parameters.genome.species`	Accepted value: string; minimum string length: 1 Requirement: Required Description: Ensembl species name, such as Homo_sapiens.

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
`dna`	Producer output: download-genome.`dna` Shared config source: `steps.create-target-gene.inputs.dna.path` or `steps.create-target-gene.inputs.dna.from` Format: gzip-compressed FASTA reference Description: Primary assembly FASTA from download-genome.
`cdna`	Producer output: download-genome.`cdna` Shared config source: `steps.create-target-gene.inputs.cdna.path` or `steps.create-target-gene.inputs.cdna.from` Format: gzip-compressed FASTA reference Description: cDNA FASTA from download-genome.
`annotation`	Producer output: download-genome.`annotation` Shared config source: `steps.create-target-gene.inputs.annotation.path` or `steps.create-target-gene.inputs.annotation.from` Format: gzip-compressed GTF Description: GTF annotation file from download-genome.
`db`	Producer output: download-genome.`db` Shared config source: `steps.create-target-gene.inputs.db.path` or `steps.create-target-gene.inputs.db.from` Format: SQLite gffutils database Description: Reusable annotation database from download-genome.

Example path-override configuration:

steps:
  create-target-gene:
    inputs:
      dna:
        path: /path/to/dna.fa
      cdna:
        path: /path/to/cdna.fa
      annotation:
        path: /path/to/annotation
      db:
        path: /path/to/db

Resources

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

Resource setting	Details
`memory_mb`	Step override: `resources.create-target-gene.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
`target_gene`	Format: JSON — `TargetGene` Description: Serialized target gene object. Path template: `{assembly}/{source}/{release}/targets/{target}/{target}_k{k}_{region}.json` Example path: `GRCh38/ensembl/114/targets/ENSG00000133703/ENSG00000133703_k16_pre-mrna.json`
`fasta`	Format: plain FASTA reference Description: Full pre-mRNA sequence, distinct exon sequences, or spliced transcript sequences according to the selected target region. Path template: `{assembly}/{source}/{release}/targets/{target}/{target}_k{k}_{region}.fa` Example path: `GRCh38/ensembl/114/targets/ENSG00000133703/ENSG00000133703_k16_pre-mrna.fa`

The step exposes target_gene as JSON and fasta as a plain FASTA file. For pre-mrna, the FASTA contains the full gene sequence as one record. For exonic, it contains one record per distinct exon ID, in genomic order, with exon ID breaking ties at the same locus. For transcriptomic, it contains one spliced sequence per transcript, ordered by transcript ID. The FASTA uses the same destination stem as the JSON file.

All records use the gene, exon, or transcript ID as their FASTA identifier, followed by the same description format: GENE_NAME gene=GENE_ID locus=CHR:START-END:STRAND. Coordinates are 1-based and inclusive; a transcript’s locus describes its full genomic span, including introns, while its sequence is spliced.