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| author | Muriithi Frederick Muriuki | 2021-08-31 10:50:56 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-08-31 10:50:56 +0300 |
| commit | e441509a59c20a051fd5ab94710513f1968a5e02 (patch) | |
| tree | 88da10c528f6d4cee8cbb111d83c47a4bf9b555a /gn3/db | |
| parent | c3f8013347e3e8850c90cb787edb2bec1f367f7d (diff) | |
| download | genenetwork3-e441509a59c20a051fd5ab94710513f1968a5e02.tar.gz | |
Update `heatmap_data` function: remove extraneous data
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: update function
* gn3/db/traits.py: new function
Remove extraneous data and arguments from the function.
- Load the genotype file
- Generate traits file
- Provide both raw traits data, and exported traits data in return
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/traits.py | 5 |
1 files changed, 5 insertions, 0 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 1031e44..ccb101a 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,4 +1,5 @@ """This class contains functions relating to trait data manipulation""" +from gn3.settings import TMPDIR from typing import Any, Dict, Union, Sequence from gn3.function_helpers import compose from gn3.db.datasets import retrieve_trait_dataset @@ -666,3 +667,7 @@ def retrieve_trait_data(trait: dict, conn: Any, strainlist: Sequence[str] = tupl {k:v for k, v in x.items() if x != "strain_name"}), data))} return {} + +def generate_traits_filename(base_path: str = TMPDIR): + return "{}/traits_test_file_{}.txt".format( + os.path.abspath(base_path), random_string(10)) |