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authorMuriithi Frederick Muriuki2021-08-12 13:09:32 +0300
committerMuriithi Frederick Muriuki2021-08-12 13:09:32 +0300
commit3420e378a614f1ecec85f633cd9f202764a54eda (patch)
treed003bc0b46635045047b890e39a0bdd2243fbfec /gn3/computations/heatmap.py
parentd97e3141554c3a13a1ec163373b19b9552a79fb0 (diff)
downloadgenenetwork3-3420e378a614f1ecec85f633cd9f202764a54eda.tar.gz
Fix linting errors
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix some errors caught by the linter.
Diffstat (limited to 'gn3/computations/heatmap.py')
-rw-r--r--gn3/computations/heatmap.py79
1 files changed, 40 insertions, 39 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
index 1b7dfb7..a0e778a 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/computations/heatmap.py
@@ -57,26 +57,24 @@ def export_trait_data(
return tuple(sample_data)
def __exporter(accumulator, strain):
- if tdata.has_key(strain):
+ # pylint: disable=[R0911]
+ if trait_data.has_key(strain):
if dtype == "val":
- return accumulator + (tdata[strain]["val"], )
+ return accumulator + (trait_data[strain]["val"], )
if dtype == "var":
- return accumulator + (tdata[strain]["var"], )
+ return accumulator + (trait_data[strain]["var"], )
if dtype == "N":
- return tdata[strain]["ndata"]
+ return trait_data[strain]["ndata"]
if dtype == "all":
- return accumulator + __export_all_types(
- accumulator, tdata, strain)
- else:
- raise KeyError("Type `%s` is incorrect" % dtype)
- else:
- if var_exists and n_exists:
- return accumulator + (None, None, None)
- if var_exists or n_exists:
- return accumulator + (None, None)
- return accumulator + (None,)
+ return accumulator + __export_all_types(trait_data, strain)
+ raise KeyError("Type `%s` is incorrect" % dtype)
+ if var_exists and n_exists:
+ return accumulator + (None, None, None)
+ if var_exists or n_exists:
+ return accumulator + (None, None)
+ return accumulator + (None,)
- return reduce(__exporter(strain), strainlist, tuple())
+ return reduce(__exporter, strainlist, tuple())
def trait_display_name(trait: Dict):
"""
@@ -96,12 +94,11 @@ def trait_display_name(trait: Dict):
return "%s::%s" % (
trait["db"]["displayname"],
desc[:desc.index('entered')].strip())
- else:
- prefix = "%s::%s" % (
- trait["db"]["dataset_name"], trait["trait_name"])
- if trait["cellid"]:
- return "%s::%s" % (prefix, trait["cellid"])
- return prefix
+ prefix = "%s::%s" % (
+ trait["db"]["dataset_name"], trait["trait_name"])
+ if trait["cellid"]:
+ return "%s::%s" % (prefix, trait["cellid"])
+ return prefix
return trait["description"]
def cluster_traits(traits_data_list: Sequence[Dict]):
@@ -114,21 +111,21 @@ def cluster_traits(traits_data_list: Sequence[Dict]):
"""
def __compute_corr(tdata_i, tdata_j):
if tdata_j[0] < tdata_i[0]:
- corr, nOverlap = compute_correlation(tdata_i, tdata_j)
+ corr_vals = compute_correlation(tdata_i, tdata_j)
+ corr = corr_vals[0]
if (1 - corr) < 0:
return 0.0
return 1 - corr
return 0.0
def __cluster(tdata_i):
- res2 = tuple(
- __compute_corr(tdata_i, tdata_j) for tdata_j in enumerate(traits))
+ return tuple(
+ __compute_corr(tdata_i, tdata_j)
+ for tdata_j in enumerate(traits_data_list))
return tuple(__cluster(tdata_i) for tdata_i in enumerate(traits_data_list))
-def heatmap_data(
- fd, search_result, conn: Any, colorScheme=None, userPrivilege=None,
- userName=None):
+def heatmap_data(formd, search_result, conn: Any):
"""
heatmap function
@@ -144,13 +141,17 @@ def heatmap_data(
PARAMETERS:
TODO: Elaborate on the parameters here...
"""
- cluster_checked = fd.formdata.getvalue("clusterCheck", "")
- strainlist = [strain for strain in fd.strainlist if strain not in fd.parlist]
- genotype = fd.genotype
+ 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, export_trait_data(retrieve_trait_data(trait), strainlist))
+ return (
+ trait,
+ export_trait_data(retrieve_trait_data(trait, conn), strainlist))
traits_details = [
__retrieve_traitlist_and_datalist(threshold, fullname)
@@ -159,18 +160,18 @@ def heatmap_data(
traits_data_list = map(lambda x: x[1], traits_details)
return {
- "target_description_checked": fd.formdata.getvalue(
+ "target_description_checked": formd.formdata.getvalue(
"targetDescriptionCheck", ""),
"cluster_checked": cluster_checked,
"slink_data": (
- slink(cluster_traits(traits_list, strainlist))
- if cluster_checked else False)
- "sessionfile": fd.formdata.getvalue("session"),
+ slink(cluster_traits(traits_data_list))
+ if cluster_checked else False),
+ "sessionfile": formd.formdata.getvalue("session"),
"genotype": genotype,
- "nLoci": sum(map(lambda x: len(x), genotype))
+ "nLoci": sum(map(len, genotype)),
"strainlist": strainlist,
- "ppolar": fd.ppolar,
- "mpolar":fd.mpolar,
- "traits_list": traits_list
+ "ppolar": formd.ppolar,
+ "mpolar":formd.mpolar,
+ "traits_list": traits_list,
"traits_data_list": traits_data_list
}