From f6bec83803d2e865ebab14effa483930069f5be1 Mon Sep 17 00:00:00 2001 From: Laura Luebbert Date: Sat, 11 Mar 2023 12:45:46 -0800 Subject: [PATCH] Updated gget info pdb oiutput unittest fixtures --- docs/src/info.md | 2 +- docs/src/updates.md | 2 +- gget/utils.py | 3 +++ 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/src/info.md b/docs/src/info.md index ab758150..309d0dcf 100644 --- a/docs/src/info.md +++ b/docs/src/info.md @@ -14,7 +14,7 @@ Python: `save=True` will save the output in the current working directory. **Flags** `-pdb` `--pdb` -Include PDB IDs in output. +Include PDB IDs in output (might increase runtime). `-eo` `--ensembl_only` Only return results from Ensembl (excludes results from UniProt, NCBI and PDB, but runs significantly faster). diff --git a/docs/src/updates.md b/docs/src/updates.md index 09a6c561..abcd380b 100644 --- a/docs/src/updates.md +++ b/docs/src/updates.md @@ -1,6 +1,6 @@ ## ✨ What's new **Version ≥ 0.27.3:** -- [`gget info`](./info.md) now excludes PDB IDs by default to increase speed (PDB results can be included using flag `--pdb`). +- [`gget info`](./info.md) excludes PDB IDs by default to increase speed (PDB results can be included using flag `--pdb` / `pdb=True`). **Version ≥ 0.27.2:** - Updated [`gget alphafold`](./alphafold.md) to [DeepMind's AlphaFold v2.3.0](https://github.com/deepmind/alphafold/releases/tag/v2.3.0) (including new arguments `multimer_for_monomer` and `multimer_recycles`) diff --git a/gget/utils.py b/gget/utils.py index c07ae3e9..5caf77c3 100644 --- a/gget/utils.py +++ b/gget/utils.py @@ -490,6 +490,9 @@ def get_pdb_ids(ens_id): """ Function to fetch all PDB IDs linked to an Ensembl ID. using the PDBe API https://wwwdev.ebi.ac.uk/pdbe/aggregated-api/mappings/ensembl_to_pdb/[ens_id] + + API documentation: + https://www.ebi.ac.uk/pdbe/aggregated-api/#/SIFTS/get_ensembl_to_pdb_mappings_api_mappings_ensembl_to_pdb__gene_id__get """ res = requests.get(ENS_TO_PDB_API + ens_id)