From a3365dae23f204e489939d3defc55edc1b4872d8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 1 Oct 2018 16:09:47 +0000
Subject: - Can now remove cofactors from correlation scatterplot and select
 them by just clicking their row in collection

- Cofactor color picker now works in Safari/Macs

- Displays N for relevant samples in trait page sample table

- Don't show bar chart when N>256

- Mapping loading page contents better centered

- Anonymous collections timeout correctly listed as 30 days now

- Minor allele frequency can actually be changed for GEMMA now (previously didn't work)

- Fixed transcript position marker location for mapping results

- Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password

- Users can now map with submitted traits

- Histogram width changes depending upon number of bins (need to improve this still)

- Improved Q-q plot (previously called "probability plot")
---
 wqflask/maintenance/convert_geno_to_bimbam.py       | 2 ++
 wqflask/maintenance/gen_select_dataset.py           | 2 +-
 wqflask/maintenance/generate_kinship_from_bimbam.py | 2 ++
 3 files changed, 5 insertions(+), 1 deletion(-)

(limited to 'wqflask/maintenance')

diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 45522705..a5d2d12a 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -154,6 +154,8 @@ class ConvertGenoFile(object):
             if not input_file.endswith(('geno', '.geno.gz')):
                 continue
             group_name = ".".join(input_file.split('.')[:-1])
+            if group_name == "HSNIH-Palmer":
+                continue
             geno_output_file = os.path.join(new_directory, group_name + "_geno.txt")
             pheno_output_file = os.path.join(new_directory, group_name + "_pheno.txt")
             snp_output_file = os.path.join(new_directory, group_name + "_snps.txt")
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 18b2dac9..55c642a4 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -219,7 +219,7 @@ def build_datasets(species, group, type_name):
         if group == 'MDP':
             dataset_text = "Mouse Phenome Database"
         else:
-            dataset_text = "%s Published Phenotypes" % group
+            dataset_text = "%s Phenotypes" % group
 
     elif type_name == "Genotypes":
         Cursor.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index f322341d..ad0eb036 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -32,6 +32,8 @@ class GenerateKinshipMatrices(object):
             if not input_file.endswith(('geno', '.geno.gz')):
                 continue
             group_name = ".".join(input_file.split('.')[:-1])
+            if group_name == "HSNIH-Palmer":
+                continue
             geno_input_file = os.path.join(bimbam_dir, group_name + "_geno.txt")
             pheno_input_file = os.path.join(bimbam_dir, group_name + "_pheno.txt")
             convertob = GenerateKinshipMatrices(group_name, geno_input_file, pheno_input_file)
-- 
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