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.

1 files changed, 68 insertions, 0 deletions

diff --git a/gn2/wqflask/correlation/correlation_functions.py b/gn2/wqflask/correlation/correlation_functions.py
new file mode 100644
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+++ b/gn2/wqflask/correlation/correlation_functions.py
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+# 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 Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+
+
+from gn2.base.mrna_assay_tissue_data import MrnaAssayTissueData
+from gn3.computations.correlations import compute_corr_coeff_p_value
+from gn2.wqflask.database import database_connection
+from gn2.utility.tools import get_setting
+
+#####################################################################################
+# Input: primaryValue(list): one list of expression values of one probeSet,
+#       targetValue(list): one list of expression values of one probeSet,
+#               method(string): indicate correlation method ('pearson' or 'spearman')
+# Output: corr_result(list): first item is Correlation Value, second item is tissue number,
+#                           third item is PValue
+# Function: get correlation value,Tissue quantity ,p value result by using R;
+# Note : This function is special case since both primaryValue and targetValue are from
+# the same dataset. So the length of these two parameters is the same. They are pairs.
+# Also, in the datatable TissueProbeSetData, all Tissue values are loaded based on
+# the same tissue order
+#####################################################################################
+
+
+def cal_zero_order_corr_for_tiss(primary_values, target_values, method="pearson"):
+    """function use calls gn3 to compute corr,p_val"""
+
+    (corr_coeff, p_val) = compute_corr_coeff_p_value(
+        primary_values=primary_values, target_values=target_values, corr_method=method)
+
+    return (corr_coeff, len(primary_values), p_val)
+
+########################################################################################################
+# input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
+# output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
+#        key is symbol, value is one list of expression values of one probeSet.
+# function: wrapper function for getSymbolValuePairDict function
+#          build gene symbol list if necessary, cut it into small lists if necessary,
+#          then call getSymbolValuePairDict function and merge the results.
+########################################################################################################
+
+
+def get_trait_symbol_and_tissue_values(symbol_list=None):
+    with database_connection(get_setting("SQL_URI")) as conn:
+        tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list, conn=conn)
+        if len(tissue_data.gene_symbols) > 0:
+            results = tissue_data.get_symbol_values_pairs()
+            return results