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authorArun Isaac2023-12-29 18:55:37 +0000
committerArun Isaac2023-12-29 19:01:46 +0000
commit204a308be0f741726b9a620d88fbc22b22124c81 (patch)
treeb3cf66906674020b530c844c2bb4982c8a0e2d39 /gn2/wqflask/comparison_bar_chart
parent83062c75442160427b50420161bfcae2c5c34c84 (diff)
downloadgenenetwork2-204a308be0f741726b9a620d88fbc22b22124c81.tar.gz
Namespace all modules under gn2.
We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service.
Diffstat (limited to 'gn2/wqflask/comparison_bar_chart')
-rw-r--r--gn2/wqflask/comparison_bar_chart/__init__.py0
-rw-r--r--gn2/wqflask/comparison_bar_chart/comparison_bar_chart.py95
2 files changed, 95 insertions, 0 deletions
diff --git a/gn2/wqflask/comparison_bar_chart/__init__.py b/gn2/wqflask/comparison_bar_chart/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/gn2/wqflask/comparison_bar_chart/__init__.py
diff --git a/gn2/wqflask/comparison_bar_chart/comparison_bar_chart.py b/gn2/wqflask/comparison_bar_chart/comparison_bar_chart.py
new file mode 100644
index 00000000..3fb3cb40
--- /dev/null
+++ b/gn2/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -0,0 +1,95 @@
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Dr. Robert W. Williams at rwilliams@uthsc.edu
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+
+from pprint import pformat as pf
+
+from gn2.base.trait import create_trait
+from gn2.base import data_set
+from gn2.utility import webqtlUtil, helper_functions, corr_result_helpers
+import gn2.utility.webqtlUtil # this is for parallel computing only.
+from gn2.wqflask.correlation import correlation_functions
+
+from flask import Flask, g
+
+
+class ComparisonBarChart:
+
+ def __init__(self, start_vars):
+ trait_db_list = [trait.strip()
+ for trait in start_vars['trait_list'].split(',')]
+
+ helper_functions.get_trait_db_obs(self, trait_db_list)
+
+ self.all_sample_list = []
+ self.traits = []
+ self.insufficient_shared_samples = False
+ # ZS: Getting initial group name before verifying all traits are in the same group in the following loop
+ this_group = self.trait_list[0][1].group.name
+ for trait_db in self.trait_list:
+
+ if trait_db[1].group.name != this_group:
+ self.insufficient_shared_samples = True
+ break
+ else:
+ this_group = trait_db[1].group.name
+ this_trait = trait_db[0]
+ self.traits.append(this_trait)
+
+ this_sample_data = this_trait.data
+
+ for sample in this_sample_data:
+ if sample not in self.all_sample_list:
+ self.all_sample_list.append(sample)
+
+ if self.insufficient_shared_samples:
+ pass
+ else:
+ self.sample_data = []
+ for trait_db in self.trait_list:
+ this_trait = trait_db[0]
+ this_sample_data = this_trait.data
+
+ this_trait_vals = []
+ for sample in self.all_sample_list:
+ if sample in this_sample_data:
+ this_trait_vals.append(this_sample_data[sample].value)
+ else:
+ this_trait_vals.append('')
+ self.sample_data.append(this_trait_vals)
+
+ self.js_data = dict(traits=[trait.name for trait in self.traits],
+ samples=self.all_sample_list,
+ sample_data=self.sample_data,)
+
+ def get_trait_db_obs(self, trait_db_list):
+
+ self.trait_list = []
+ for i, trait_db in enumerate(trait_db_list):
+ if i == (len(trait_db_list) - 1):
+ break
+ trait_name, dataset_name = trait_db.split(":")
+ #print("dataset_name:", dataset_name)
+ dataset_ob = data_set.create_dataset(dataset_name)
+ trait_ob = create_trait(dataset=dataset_ob,
+ name=trait_name,
+ cellid=None)
+ self.trait_list.append((trait_ob, dataset_ob))
+
+ #print("trait_list:", self.trait_list)