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authorMuriithi Frederick Muriuki2021-08-31 10:50:56 +0300
committerMuriithi Frederick Muriuki2021-08-31 10:50:56 +0300
commite441509a59c20a051fd5ab94710513f1968a5e02 (patch)
tree88da10c528f6d4cee8cbb111d83c47a4bf9b555a
parentc3f8013347e3e8850c90cb787edb2bec1f367f7d (diff)
downloadgenenetwork3-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
-rw-r--r--gn3/computations/heatmap.py42
-rw-r--r--gn3/db/traits.py5
2 files changed, 27 insertions, 20 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
index e0ff05b..92014cf 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/computations/heatmap.py
@@ -6,8 +6,12 @@ generate various kinds of heatmaps.
from functools import reduce
from typing import Any, Dict, Sequence
from gn3.computations.slink import slink
-from gn3.db.traits import retrieve_trait_data, retrieve_trait_info
from gn3.computations.correlations2 import compute_correlation
+from gn3.db.genotypes import build_genotype_file, load_genotype_samples
+from gn3.db.traits import (
+ retrieve_trait_data,
+ retrieve_trait_info,
+ generate_traits_filename)
def export_trait_data(
trait_data: dict, strainlist: Sequence[str], dtype: str = "val",
@@ -125,7 +129,7 @@ def cluster_traits(traits_data_list: Sequence[Dict]):
return tuple(__cluster(tdata_i) for tdata_i in enumerate(traits_data_list))
-def heatmap_data(formd, search_result, conn: Any):
+def heatmap_data(traits_names, conn: Any):
"""
heatmap function
@@ -142,39 +146,37 @@ def heatmap_data(formd, search_result, conn: Any):
TODO: Elaborate on the parameters here...
"""
threshold = 0 # webqtlConfig.PUBLICTHRESH
- cluster_checked = formd.formdata.getvalue("clusterCheck", "")
- strainlist = [
- strain for strain in formd.strainlist if strain not in formd.parlist]
- genotype = formd.genotype
-
def __retrieve_traitlist_and_datalist(threshold, fullname):
trait = retrieve_trait_info(threshold, fullname, conn)
return (trait, retrieve_trait_data(trait, conn))
traits_details = [
__retrieve_traitlist_and_datalist(threshold, fullname)
- for fullname in search_result]
+ for fullname in traits_names]
traits_list = tuple(x[0] for x in traits_details)
traits_data_list = [x[1] for x in traits_details]
exported_traits_data_list = tuple(
export_trait_data(td, strainlist) for td in traits_data_list)
+ genotype_filename = build_genotype_file(traits_list[0]["riset"])
+ strainlist = load_genotype_samples(genotype_filename)
+ slink_data = slink(cluster_traits(exported_traits_data_list))
+ ordering_data = compute_heatmap_order(slink_data)
+ strains_and_values = retrieve_strains_and_values(
+ orders, strainlist, exported_traits_data_list)
+ strains_values = strains_and_values[0][1]
+ trait_values = [t[2] for t in strains_and_values]
+ traits_filename = generate_traits_filename()
+ generate_traits_file(strains_values, trait_values, traits_filename)
return {
- "target_description_checked": formd.formdata.getvalue(
- "targetDescriptionCheck", ""),
- "cluster_checked": cluster_checked,
- "slink_data": (
- slink(cluster_traits(exported_traits_data_list))
- if cluster_checked else False),
- "sessionfile": formd.formdata.getvalue("session"),
- "genotype": genotype,
- "nLoci": sum(map(len, genotype)),
+ "slink_data": slink_data,
+ "ordering_data": ordering_data,
"strainlist": strainlist,
- "ppolar": formd.ppolar,
- "mpolar":formd.mpolar,
+ "genotype_filename": genotype_filename,
"traits_list": traits_list,
"traits_data_list": traits_data_list,
- "exported_traits_data_list": exported_traits_data_list
+ "exported_traits_data_list": exported_traits_data_list,
+ "traits_filename": traits_filename
}
def compute_heatmap_order(
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))