API
Main Entry Point
iduna runs the full ThorAxe plus MMseqs2/HMMER pipeline by default. Use no_expansion=true to stop after the ThorAxe MSA stage; in that case result.expansion === nothing, load_seed_msa(result) remains available, and load_expanded_msa(result) throws a guidance error.
Iduna.iduna — Function
iduna(; id, mmseqs_db=nothing, no_expansion=false, kwargs...) -> IdunaResult
iduna(id; mmseqs_db=nothing, no_expansion=false, kwargs...) -> IdunaResultBuild one ThorAxe-based MSA from a UniProt accession or an Ensembl transcript ID and, by default, expand it with MMseqs2/HMMER. Set no_expansion=true to stop after the ThorAxe MSA stage without requiring an MMseqs2 database.
The function is file-first: every external tool writes its inputs, outputs, and logs under workdir, and the returned IdunaResult stores paths plus the resolved identifiers and validation statistics.
orthology controls the ThorAxe relationship filter ("1:1", "1:n", or "m:n"). By default, Iduna filters the ThorAxe species list with Ensembl homology and then filters against currently available BioMart Ensembl Gene datasets before transcript_query. transcript_query_timeout_seconds limits each Ensembl query attempt. Iduna retries that step and can retry without specieslist after a timeout. Set thoraxe_timeout_seconds to give the baseline and PID ThorAxe runs the same kind of wall-clock guard. Pass thoraxe_input_dir to reuse a complete transcriptquery bundle instead of fetching it again. Set centroids=true to also save the centroid-level MSA before MMseqs2 expands centroid hits to cluster members; the main expansion and validation still use the full expanded MSA. centroids=true requires expansion and cannot be combined with `noexpansion=true`.
Iduna.load_seed_msa — Function
load_seed_msa(result; keepinserts=true)Load the selected ThorAxe seed MSA from an IdunaResult as a MIToS MSA.
Iduna.load_expanded_msa — Function
load_expanded_msa(result; keepinserts=true)Load the expanded match-column MSA from an IdunaResult as a MIToS MSA.
Result Types
Iduna.Utils.ResolvedTarget — Type
ResolvedTargetResolved identifiers and sequence-validation metadata for one input ID.
Iduna.Utils.SeedSelection — Type
SeedSelectionThe ThorAxe PID seed chosen for expansion, plus the summary values used to pick it.
Iduna.Utils.ThorAxeMSAResult — Type
ThorAxeMSAResultPaths and metadata produced by the ThorAxe MSA-building stage.
Iduna.Utils.ExpansionResult — Type
ExpansionResultPaths and hit counts produced by the MMseqs2/HMMER expansion stage.
Iduna.Utils.ValidationResult — Type
ValidationResultSeed and expanded-MSA statistics plus optional query-vs-UniProt checks.
Iduna.Utils.IdunaResult — Type
IdunaResultTop-level result returned by Iduna.iduna. It keeps the full pipeline status and links to the per-stage result objects. expansion is nothing when the run was requested with no_expansion=true.