Output Formats

The primary output of eris is a tabular TSV report detailing the evolutionary context of every assembled locus.

Represents a single structural variant or passenger gene record in the eris TSV report.

Attributes:

Name	Type	Description
`locus_id`	`str`	Unique identifier for the assembled structural variant locus.
`target`	`str`	The mobile genetic element(s) or query sequences found in this locus.
`gene_id`	`str`	The identifier of the contextual passenger or flanking gene.
`context`	`str`	The spatial relationship (e.g., INSIDE, UPSTREAM) of the gene to the target.
`dist_bp`	`int`	Distance in base pairs between the gene and the target element.
`topo_hops`	`int`	Number of graph nodes traversed to find this gene (0 if on the same contig).
`orientation`	`str`	Strand orientation of the gene relative to the target (same or opposite).
`effect`	`str`	Biological impact of the insertion on the gene (e.g., TRUNCATED, NONE).
`fractional_depth`	`float`	The relative read depth of the variant path compared to the source contig, indicating sub-clonal abundance.

Source code in src/eris/io.py

@dataclass(slots=True, frozen=True)
class ReportRow:
    """
    Represents a single structural variant or passenger gene record in the eris TSV report.

    Attributes:
        locus_id: Unique identifier for the assembled structural variant locus.
        target: The mobile genetic element(s) or query sequences found in this locus.
        gene_id: The identifier of the contextual passenger or flanking gene.
        context: The spatial relationship (e.g., INSIDE, UPSTREAM) of the gene to the target.
        dist_bp: Distance in base pairs between the gene and the target element.
        topo_hops: Number of graph nodes traversed to find this gene (0 if on the same contig).
        orientation: Strand orientation of the gene relative to the target (same or opposite).
        effect: Biological impact of the insertion on the gene (e.g., TRUNCATED, NONE).
        fractional_depth: The relative read depth of the variant path compared to the source contig, indicating sub-clonal abundance.
    """
    locus_id: str
    target: str
    gene_id: str
    context: str
    dist_bp: int
    topo_hops: int
    orientation: str
    effect: str
    fractional_depth: float

    @classmethod
    def header(cls) -> str:
        """Returns the TSV header string dynamically generated from the dataclass fields."""
        return "\t".join(cls.__annotations__.keys()) + "\n"

    def to_tsv(self) -> str:
        """Formats the row data into a tab-separated string."""
        return f"{self.locus_id}\t{self.target}\t{self.gene_id}\t{self.context}\t{self.dist_bp}\t{self.topo_hops}\t{self.orientation}\t{self.effect}\t{self.fractional_depth}\n"