Ensembl Plants: Assembly
ensembl_plants_assemblyRetrieve an organism's Ensembl assembly: name, GCA accession, date, karyotype, and all top-level sequence regions with lengths. Karyotype regions come first to plan region walks.
Instructions
Describe an organism's Ensembl assembly (rest.ensembl.org /info/assembly; free, no key): assembly name, GCA accession and date, the karyotype, and every top-level seq-region with its length. The names are the region values ensembl_region_query takes, and a start past a region's length is refused there, so a region walk can be planned before the first call. Karyotype regions come first, in karyotype order, then unplaced scaffolds and contigs, longest first. Names are Ensembl's: tomato's chromosomes are CM001064.4 and so on, not '1'. coord_system labels differ between assemblies (chromosome, scaffold, supercontig, primary_assembly), so in_karyotype, not coord_system, says which regions are chromosomes. total counts every region before limit; truncated=true when limit cut some off (soybean has over 1,100).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | ||
| organism | Yes | Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| total | Yes | How many top-level regions exist upstream for this query, all pages (pre-cap) (#123) | |
| regions | Yes | Karyotype regions first, in karyotype order; then the rest, longest first | |
| organism | Yes | Canonical organism slug | |
| returned | Yes | Rows in this payload (#123) | |
| karyotype | Yes | The chromosomes, in Ensembl's karyotype order | |
| truncated | Yes | True when limit cut regions off | |
| assembly_date | Yes | Assembly date as Ensembl gives it (YYYY-MM); null when Ensembl gives none | |
| assembly_name | Yes | Assembly name, e.g. TAIR10, IRGSP-1.0 | |
| upstream_version | No | Ensembl release that produced THIS response, — always null today: this backend states no release on its responses; upstream_release(backend='ensembl_plants') reports the release its own endpoint calls current at query time, or why there is none. null means Ensembl did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered. | |
| assembly_accession | Yes | INSDC assembly accession (GCA_...) |