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authorLei Yan2013-09-20 17:20:52 -0500
committerLei Yan2013-09-20 17:20:52 -0500
commit183f9a0ba19b6fcdf1475285af1bb1fcd45a9442 (patch)
tree54bb010628a427b033eb8e10f5a7402af89fab48
parentaf24c0d610d9a2189f86677e4f23deb372ee2bf7 (diff)
downloadgenenetwork2-183f9a0ba19b6fcdf1475285af1bb1fcd45a9442.tar.gz
Tissue correlation results work for sample r/rho correlation page
and are written to the template
-rw-r--r--misc/gn_installation_notes.txt14
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py152
-rw-r--r--wqflask/wqflask/correlation/correlation_functions.py12
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py65
-rw-r--r--wqflask/wqflask/templates/correlation_page.html9
5 files changed, 157 insertions, 95 deletions
diff --git a/misc/gn_installation_notes.txt b/misc/gn_installation_notes.txt
index 6329586f..a73e7d4f 100644
--- a/misc/gn_installation_notes.txt
+++ b/misc/gn_installation_notes.txt
@@ -272,6 +272,12 @@ sudo apt-get install r-base-dev
===========================================
+Installing rpy2
+
+pip install rpy2
+
+===========================================
+
Install Parallel Python (pp)
wget http://www.parallelpython.com/downloads/pp/pp-1.6.3.tar.gz
@@ -303,7 +309,13 @@ To get server running:
!If having seemingly inexplicable problems with imports, make sure I've started the environment!
Start up virtual environment:
-source ~/ve27/bin/activate
+source ~/ve27/bin/activate==============
+
+Install requests
+
+pip install requests
+
+=======================
To set WQFLASK_SETTINGS environment variable:
export WQFLASK_SETTINGS=~/zach_settings.py (or wherever file is located)
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 8ae71858..7eb07028 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -4,11 +4,13 @@ import collections
from flask import g
-from utility import dbtools
-from uitility import Bunch
+from utility import db_tools
+from utility import Bunch
from MySQLdb import escape_string as escape
+from pprint import pformat as pf
+
class MrnaAssayTissueData(object):
def __init__(self, gene_symbols=None):
@@ -35,14 +37,15 @@ class MrnaAssayTissueData(object):
# Note that inner join is necessary in this query to get distinct record in one symbol group
# with highest mean value
# Due to the limit size of TissueProbeSetFreezeId table in DB,
- # performance of inner join is acceptable.
+ # performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
+ print("len(gene_symbols): ", len(gene_symbols))
if len(gene_symbols) == 0:
query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
'''
else:
- in_clause = dbtools.create_in_clause(gene_symbols)
+ in_clause = db_tools.create_in_clause(gene_symbols)
query += ''' Symbol in {} group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
@@ -51,17 +54,19 @@ class MrnaAssayTissueData(object):
results = g.db.execute(query).fetchall()
for result in results:
- symbol = item[0]
- gene_symbols.append(symbol)
- symbol = symbol.lower()
-
- self.data[symbol].gene_id = result.GeneId
- self.data[symbol].data_id = result.DataId
- self.data[symbol].chr = result.Chr
- self.data[symbol].mb = result.Mb
- self.data[symbol].description = result.description
- self.data[symbol].probe_target_description = result.Probe_Target_Description
+ symbol = result[0]
+ if symbol in gene_symbols:
+ #gene_symbols.append(symbol)
+ symbol = symbol.lower()
+
+ self.data[symbol].gene_id = result.GeneId
+ self.data[symbol].data_id = result.DataId
+ self.data[symbol].chr = result.Chr
+ self.data[symbol].mb = result.Mb
+ self.data[symbol].description = result.description
+ self.data[symbol].probe_target_description = result.Probe_Target_Description
+ #print("self.data: ", pf(self.data))
###########################################################################
#Input: cursor, symbolList (list), dataIdDict(Dict)
@@ -70,65 +75,72 @@ class MrnaAssayTissueData(object):
#function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
#Attention! All keys are lower case!
###########################################################################
- def get_symbol_value_pairs(self):
-
- id_list = [self.tissue_data[symbol.lower()].data_id for item in self.tissue_data]
-
- symbol_value_pairs = {}
- value_list=[]
- query = """SELECT value, id
- FROM TissueProbeSetData
- WHERE Id IN {}""".format(create_in_clause(id_list))
-
- try :
- results = g.db.execute(query).fetchall()
- for result in results:
- value_list.append(result.value)
- symbol_value_pairs[symbol] = value_list
- except:
- symbol_value_pairs[symbol] = None
-
- #for symbol in symbol_list:
- # if tissue_data.has_key(symbol):
- # data_id = tissue_data[symbol].data_id
- #
- # query = """select value, id
- # from TissueProbeSetData
- # where Id={}""".format(escape(data_id))
- # try :
- # results = g.db.execute(query).fetchall()
- # for item in results:
- # item = item[0]
- # value_list.append(item)
- # symbol_value_pairs[symbol] = value_list
- # value_list=[]
- # except:
- # symbol_value_pairs[symbol] = None
+ def get_symbol_values_pairs(self):
+ id_list = [self.data[symbol].data_id for symbol in self.data]
+
+ symbol_values_dict = {}
+
+ query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
+ FROM TissueProbeSetXRef, TissueProbeSetData
+ WHERE TissueProbeSetData.Id IN {} and
+ TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
+
+ results = g.db.execute(query).fetchall()
+ for result in results:
+ if result.Symbol.lower() not in symbol_values_dict:
+ symbol_values_dict[result.Symbol.lower()] = [result.value]
+ else:
+ symbol_values_dict[result.Symbol.lower()].append(result.value)
+
+ #for symbol in self.data:
+ # data_id = self.data[symbol].data_id
+ # symbol_values_dict[symbol] = self.get_tissue_values(data_id)
+
- return symbol_value_pairs
+ return symbol_values_dict
- ########################################################################################################
- #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):
- tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
+ #def get_tissue_values(self, data_id):
+ # """Gets the tissue values for a particular gene"""
+ #
+ # tissue_values=[]
+ #
+ # query = """SELECT value, id
+ # FROM TissueProbeSetData
+ # WHERE Id IN {}""".format(db_tools.create_in_clause(data_id))
+ #
+ # #try :
+ # results = g.db.execute(query).fetchall()
+ # for result in results:
+ # tissue_values.append(result.value)
+ # #symbol_values_dict[symbol] = value_list
+ # #except:
+ # # symbol_values_pairs[symbol] = None
+ #
+ # return tissue_values
- #symbolList,
- #geneIdDict,
- #dataIdDict,
- #ChrDict,
- #MbDict,
- #descDict,
- #pTargetDescDict = getTissueProbeSetXRefInfo(
- # GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-
- if len(tissue_data.gene_symbols):
- return get_symbol_value_pairs(tissue_data)
+########################################################################################################
+#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):
+# tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
+#
+# #symbolList,
+# #geneIdDict,
+# #dataIdDict,
+# #ChrDict,
+# #MbDict,
+# #descDict,
+# #pTargetDescDict = getTissueProbeSetXRefInfo(
+# # GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
+#
+# if len(tissue_data.gene_symbols):
+# return get_symbol_values_pairs(tissue_data)
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index 56f66810..84d47bb5 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -27,7 +27,7 @@
from __future__ import absolute_import, print_function, division
import math
-#import rpy2.robjects
+import rpy2.robjects
import pp
import string
@@ -494,7 +494,7 @@ pcor.rec <- function(x,y,z,method="p",na.rm=T){
#XZ, April 30, 2010: The input primaryTrait and targetTrait are instance of webqtlTrait
#XZ: The primaryTrait and targetTrait should have executed retrieveData function
-def calZeroOrderCorr (primaryTrait, targetTrait, method='pearson'):
+def calZeroOrderCorr(primaryTrait, targetTrait, method='pearson'):
#primaryTrait.retrieveData()
@@ -560,7 +560,7 @@ def calZeroOrderCorr (primaryTrait, targetTrait, method='pearson'):
#the same tissue order
#####################################################################################
-def calZeroOrderCorrForTiss (primaryValue=[], targetValue=[], method='pearson'):
+def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pearson'):
R_primary = rpy2.robjects.FloatVector(range(len(primaryValue)))
N = len(primaryValue)
@@ -809,6 +809,9 @@ def get_trait_symbol_and_tissue_values(symbol_list=None):
tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
+ if len(tissue_data.gene_symbols):
+ return tissue_data.get_symbol_values_pairs()
+
#symbolList,
#geneIdDict,
#dataIdDict,
@@ -818,9 +821,6 @@ def get_trait_symbol_and_tissue_values(symbol_list=None):
#pTargetDescDict = getTissueProbeSetXRefInfo(
# GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
- if len(tissue_data.gene_symbols):
- return get_symbol_value_pairs(tissue_data)
-
#limit_num=1000
#count = len(symbol_list)
#
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index b17e1db1..b9d009af 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -105,7 +105,7 @@ class CorrelationResults(object):
self.sample_data = {}
self.corr_method = start_vars['corr_sample_method']
- self.return_number = 500
+ self.return_number = 50
#The two if statements below append samples to the sample list based upon whether the user
#rselected Primary Samples Only, Other Samples Only, or All Samples
@@ -158,15 +158,27 @@ class CorrelationResults(object):
for trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
trait_object = GeneralTrait(dataset=self.dataset, name=trait, get_qtl_info=True)
+
+ print("gene symbol: ", trait_object.symbol)
+
trait_object.sample_r = self.correlation_data[trait][0]
trait_object.sample_p = self.correlation_data[trait][1]
trait_object.num_overlap = self.correlation_data[trait][2]
+ #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef,
+ #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions)
+
+
+
# Set some sane defaults
- trait_object.tissue_corr = None
- trait_object.tissue_pvalue = None
+ trait_object.tissue_corr = 0
+ trait_object.tissue_pvalue = 0
self.correlation_results.append(trait_object)
+
+ self.do_tissue_correlation_by_list()
+
+ print("self.correlation_results: ", pf(self.correlation_results))
@@ -183,7 +195,7 @@ class CorrelationResults(object):
# mb = trait_object.mb
# )
# if trait_object.mean:
- # trait_info[mean] = trait_object.mean
+ #def do_tissue_correlation_by_list(self, tissue_dataset_id):t_object.alias, # trait_info[mean] = trait_object.mean
# if hasattr(trait_object, 'mean'):
# trait_info[mean] = trait_object.mean
# if hasattr(trait_object, 'lrs'):
@@ -197,7 +209,8 @@ class CorrelationResults(object):
# correlation = float(self.correlation_data[trait][0]),
# p_value = float(self.correlation_data[trait][1]),
# symbol = trait_object.symbol,
- # alias = trait_object.alias,
+ # alias = trai
+ #def do_tissue_correlation_by_list(self, tissue_dataset_id):t_object.alias,
# description = trait_object.description,
# chromosome = trait_object.chr,
# mb = trait_object.mb
@@ -637,7 +650,15 @@ class CorrelationResults(object):
for entry in results:
trait_name, tissue_corr, tissue_pvalue = entry
tissue_corr_dict[trait_name] = (tissue_corr, tissue_pvalue)
-
+ #symbolList,
+ #geneIdDict,
+ #dataIdDict,
+ #ChrDict,
+ #MbDict,
+ #descDict,
+ #pTargetDescDict = getTissueProbeSetXRefInfo(
+ # GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
+
g.db.execute('DROP TEMPORARY TABLE {}'.format(escape(temp_table)))
return tissue_corr_dict
@@ -944,13 +965,17 @@ class CorrelationResults(object):
return (symbolCorrDict, symbolPvalueDict)
- def do_tissue_correlation_by_list(self, tissue_dataset_id):
+ def do_tissue_correlation_by_list(self, tissue_dataset_id=1):
+ """Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each"""
- trait_symbol_and_values = correlation_functions.get_trait_symbol_and_tissue_values(
- gene_name_list = [self.this_trait.symbol])
+ #Gets tissue expression values for the primary trait
+ primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
+ symbol_list = [self.this_trait.symbol])
+
+ print("primary_trait_tissue_vals: ", pf(primary_trait_tissue_vals_dict))
- if self.this_trait.symbol.lower() in trait_symbol_and_values:
- primary_trait_value = trait_symbol_and_values[self.this_trait_symbol.lower()]
+ if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
+ primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
#gene_symbol_list = []
#
@@ -960,19 +985,25 @@ class CorrelationResults(object):
gene_symbol_list = [trait.symbol for trait in self.correlation_results if trait.symbol]
- symbol_value_dict = correlation_functions.get_trait_gene_symbol_and_tissue_values(
- gene_symbol_list=gene_symbol_list)
+ corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
+ symbol_list=gene_symbol_list)
+
+ print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
for trait in self.correlation_results:
- if trait.symbol and trait.symbol.lower() in symbol_value_dict:
- this_trait_value = symbol_value_dict[trait.symbol.lower()]
+ if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict:
+ this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower()]
- result = correlation_functions.calZeroOrderCorrForTiss(primary_trait_value,
- this_trait_value,
+ result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
+ this_trait_tissue_values,
self.corr_method)
trait.tissue_corr = result[0]
trait.tissue_pvalue = result[2]
+
+ #print("trait.tissue_corr / pvalue: ", str(trait.tissue_corr) + " :: " + str(trait.tissue_pvalue))
+
+
# else:
# trait.tissue_corr = None
# trait.tissue_pvalue = None
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 53b12545..7082dbf2 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -28,10 +28,15 @@
<th>Sample r</th>
<th>N Cases</th>
<th>Sample p(r)</th>
+ <th>Tissue r</th>
+ <th>Tissue p(r)</th>
{% else %}
<th>Sample rho</th>
<th>Sample p(rho)</th>
+ <th>Tissue rho</th>
+ <th>Tissue p(rho)</th>
{% endif %}
+
</tr>
</thead>
<tbody>
@@ -41,13 +46,15 @@
<td>{{ trait.symbol }}</td>
<td>{{ trait.alias }}</td>
<td>{{ trait.description }}</td>
- <td>Chr{{ trait.chr }}:{{'%0.6f'|format(trait.mb)}}</td>
+ <td>Chr{{ trait.chr }}:{{trait.mb}}</td>
<td>{{'%0.3f'|format(trait.mean)}}</td>
<td>{{'%0.3f'|format(trait.lrs)}}</td>
<td>Chr{{ trait.locus_chr }}:{{'%0.6f'|format(trait.locus_mb)}}</td>
<td>{{'%0.3f'|format(trait.sample_r)}}</td>
<td>{{ trait.num_overlap }}</td>
<td>{{'%0.3e'|format(trait.sample_p)}}</td>
+ <td>{{'%0.3f'|format(trait.tissue_corr)}}</td>
+ <td>{{'%0.3e'|format(trait.tissue_pvalue)}}</td>
</tr>
{% endfor %}
</tbody>