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authorMuriithi Frederick Muriuki2021-08-20 14:10:45 +0300
committerMuriithi Frederick Muriuki2021-08-20 14:10:45 +0300
commit8b2c776771d2a70613a1e31d6e6671b612cfbafc (patch)
treead7ab6dcd4c43b15afdbe74322fbac76db0f34db /gn3/computations
parentded960e3d32e4d7ebe590deda27fc47175be73d9 (diff)
downloadgenenetwork3-8b2c776771d2a70613a1e31d6e6671b612cfbafc.tar.gz
Retrieve the strains with valid values
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: add function to get strains with values * tests/unit/computations/test_heatmap.py: new tests Add function to get the strains whose values are not `None` from the `trait_data` object passed in. This migrates https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L215-221 into a separate function that can handle that and be tested independently of any other code.
Diffstat (limited to 'gn3/computations')
-rw-r--r--gn3/computations/heatmap.py19
1 files changed, 19 insertions, 0 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
index 1c86261..5a3c619 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/computations/heatmap.py
@@ -203,3 +203,22 @@ def compute_heatmap_order(
return __order_maker(__order_maker(norder, slnk_dt[0]), slnk_dt[1])
return __order_maker(neworder, slink_data)
+
+def retrieve_strains_and_values(strainlist, trait_data):
+ """
+ Get the strains and their corresponding values from `strainlist` and
+ `trait_data`.
+
+ This migrates the code in
+ https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L215-221
+ """
+ def __strains_and_values(acc, i):
+ if trait_data[i] is None:
+ return acc
+ if len(acc) == 0:
+ return ((strainlist[i], ), (trait_data[i], ))
+ _strains = acc[0]
+ _vals = acc[1]
+ return (_strains + (strainlist[i], ), _vals + (trait_data[i], ))
+ return reduce(
+ __strains_and_values, range(len(strainlist)), (tuple(), tuple()))