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-rw-r--r--wqflask/wqflask/do_search.py56
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py80
-rw-r--r--wqflask/wqflask/search_results.py30
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.coffee4
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.js4
-rw-r--r--wqflask/wqflask/templates/index_page.html4
6 files changed, 114 insertions, 64 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index a2eddfc6..b390bdc4 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -20,17 +20,18 @@ class DoSearch(object):
# Used to translate search phrases into classes
search_types = dict()
- def __init__(self, search_term, search_operator, dataset):
+ def __init__(self, search_term, search_operator=None, dataset=None):
self.search_term = search_term
# Make sure search_operator is something we expect
assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator"
self.search_operator = search_operator
self.dataset = dataset
- print("self.dataset is boo: ", type(self.dataset), pf(self.dataset))
- print("self.dataset.group is: ", pf(self.dataset.group))
-
- #Get group information for dataset and the species id
- self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
+
+ if self.dataset:
+ print("self.dataset is boo: ", type(self.dataset), pf(self.dataset))
+ print("self.dataset.group is: ", pf(self.dataset.group))
+ #Get group information for dataset and the species id
+ self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
def execute(self, query):
"""Executes query and returns results"""
@@ -59,6 +60,47 @@ class DoSearch(object):
def get_search(cls, search_type):
return cls.search_types[search_type]
+class QuickMrnaAssaySearch(DoSearch):
+ """A general search for mRNA assays"""
+
+ DoSearch.search_types['quick_mrna_assay'] = "QuickMrnaAssaySearch"
+
+ base_query = """SELECT ProbeSet.Name as ProbeSet_Name,
+ ProbeSet.Chr_num as ProbeSet_Chr_Num,
+ ProbeSet.Mb as ProbeSet_Mb,
+ ProbeSet.Symbol as ProbeSet_Symbol,
+ ProbeSet.name_num as ProbeSet_name_num
+ FROM ProbeSet,
+ ProbeSetXRef,
+ ProbeSetFreeze,
+ ProbeFreeze,
+ InbredSet,
+ Species """
+
+ header_fields = ['',
+ 'Record ID',
+ 'Symbol',
+ 'Location']
+
+ def run(self):
+ """Generates and runs a search for assays across all mRNA expression datasets"""
+
+ print("Running ProbeSetSearch")
+ query = self.base_query + """WHERE (MATCH (ProbeSet.Name,
+ ProbeSet.description,
+ ProbeSet.symbol)
+ AGAINST ('%s' IN BOOLEAN MODE)) and
+ ProbeSet.Id = ProbeSetXRef.ProbeSetId and
+ ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
+ ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
+ ProbeFreeze.InbredSetId = InbredSet.Id and
+ InbredSet.SpeciesId = Species.Id
+ """ % (escape(self.search_term[0]))
+
+ print("final query is:", pf(query))
+
+ return self.execute(query)
+
class MrnaAssaySearch(DoSearch):
"""A search within an mRNA expression dataset"""
@@ -125,6 +167,8 @@ class MrnaAssaySearch(DoSearch):
return self.execute(query)
+#class QuickPhenotypeSearch(DoSearch):
+
class PhenotypeSearch(DoSearch):
"""A search within a phenotype dataset"""
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 66830662..1e689e49 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -26,42 +26,42 @@ from scipy import stats
from pprint import pformat as pf
-#from utility.benchmark import Bench
-#
-##np.seterr('raise')
-#
-#def run(pheno_vector,
-# genotype_matrix,
-# restricted_max_likelihood=True,
-# refit=False,
-# temp_data=None):
-# """Takes the phenotype vector and genotype matrix and returns a set of p-values and t-statistics
-#
-# restricted_max_likelihood -- whether to use restricted max likelihood; True or False
-# refit -- whether to refit the variance component for each marker
-# temp_data -- TempData object that stores the progress for each major step of the
-# calculations ("calculate_kinship" and "GWAS" take the majority of time)
-#
-# """
-#
-# with Bench("Calculate Kinship"):
-# kinship_matrix = calculate_kinship(genotype_matrix, temp_data)
-#
-# with Bench("Create LMM object"):
-# lmm_ob = LMM(pheno_vector, kinship_matrix)
-#
-# with Bench("LMM_ob fitting"):
-# lmm_ob.fit()
-#
-# with Bench("Doing GWAS"):
-# t_stats, p_values = GWAS(pheno_vector,
-# genotype_matrix,
-# kinship_matrix,
-# restricted_max_likelihood=True,
-# refit=False,
-# temp_data=temp_data)
-# Bench().report()
-# return t_stats, p_values
+from utility.benchmark import Bench
+
+#np.seterr('raise')
+
+def run(pheno_vector,
+ genotype_matrix,
+ restricted_max_likelihood=True,
+ refit=False,
+ temp_data=None):
+ """Takes the phenotype vector and genotype matrix and returns a set of p-values and t-statistics
+
+ restricted_max_likelihood -- whether to use restricted max likelihood; True or False
+ refit -- whether to refit the variance component for each marker
+ temp_data -- TempData object that stores the progress for each major step of the
+ calculations ("calculate_kinship" and "GWAS" take the majority of time)
+
+ """
+
+ with Bench("Calculate Kinship"):
+ kinship_matrix = calculate_kinship(genotype_matrix, temp_data)
+
+ with Bench("Create LMM object"):
+ lmm_ob = LMM(pheno_vector, kinship_matrix)
+
+ with Bench("LMM_ob fitting"):
+ lmm_ob.fit()
+
+ with Bench("Doing GWAS"):
+ t_stats, p_values = GWAS(pheno_vector,
+ genotype_matrix,
+ kinship_matrix,
+ restricted_max_likelihood=True,
+ refit=False,
+ temp_data=temp_data)
+ Bench().report()
+ return t_stats, p_values
def matrixMult(A,B):
@@ -99,8 +99,8 @@ def calculate_kinship(genotype_matrix, temp_data):
"""
n = genotype_matrix.shape[0]
m = genotype_matrix.shape[1]
- print("n is:", n)
- print("m is:", m)
+ #print("n is:", n)
+ #print("m is:", m)
keep = []
for counter in range(m):
print("type of genotype_matrix[:,counter]:", pf(genotype_matrix[:,counter]))
@@ -123,7 +123,6 @@ def calculate_kinship(genotype_matrix, temp_data):
genotype_matrix[:,counter] = (genotype_matrix[:,counter] - values_mean) / np.sqrt(vr)
percent_complete = int(round((counter/m)*45))
- print("Percent complete: ", percent_complete)
temp_data.store("percent_complete", percent_complete)
genotype_matrix = genotype_matrix[:,keep]
@@ -220,7 +219,6 @@ def GWAS(pheno_vector,
ts, ps = lmm_ob.association(x, REML=restricted_max_likelihood)
percent_complete = 45 + int(round((counter/m)*55))
- print("Percent complete: ", percent_complete)
temp_data.store("percent_complete", percent_complete)
p_values.append(ps)
@@ -279,6 +277,8 @@ class LMM:
self.K = K
self.Kva = Kva
self.Kve = Kve
+ print("self.Kva is: ", pf(self.Kva))
+ print("self.Kve is: ", pf(self.Kve))
self.Y = Y
self.X0 = X0
self.N = self.K.shape[0]
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 080568f0..2d39a711 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -45,7 +45,7 @@ class SearchResultPage():
###########################################
# Names and IDs of group / F2 set
###########################################
-
+
# All Phenotypes is a special case we'll deal with later
#if kw['dataset'] == "All Phenotypes":
# self.cursor.execute("""
@@ -57,15 +57,16 @@ class SearchResultPage():
# self.dataset_groups = map(lambda x: x[1], results)
# self.dataset_group_ids = map(lambda x: x[2], results)
#else:
-
+
self.results = []
-
+
if 'q' in kw:
- self.quick_search = True
+ #self.quick_search = True
self.search_terms = kw['q']
+ print("self.search_terms is: ", self.search_terms)
self.quick_search()
else:
- self.quick_search = False
+ #self.quick_search = False
self.search_terms = kw['search_terms']
self.dataset = create_dataset(kw['dataset'])
self.search()
@@ -98,10 +99,23 @@ class SearchResultPage():
self.trait_list.append(this_trait)
self.dataset.get_trait_info(self.trait_list, species)
-
+
def quick_search(self):
+ self.search_terms = parser.parse(self.search_terms)
+ print("After parsing:", self.search_terms)
- return True
+ for a_search in self.search_terms:
+ search_term = a_search['search_term']
+ #Do mRNA assay search
+ search_ob = do_search.DoSearch.get_search("quick_mrna_assay")
+ search_class = getattr(do_search, search_ob)
+ the_search = search_class(search_term)
+
+ self.results.extend(the_search.run())
+ print("in the search results are:", self.results)
+
+
+ #return True
#search_gene
#search_geno
@@ -114,8 +128,6 @@ class SearchResultPage():
self.search_terms = parser.parse(self.search_terms)
print("After parsing:", self.search_terms)
-
-
for a_search in self.search_terms:
print("[kodak] item is:", pf(a_search))
search_term = a_search['search_term']
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 4d678bde..6e605fa7 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -85,7 +85,7 @@ $ ->
marker_name = marker_info[2]
else
marker_name = ""
- $("#qtl_results_filter").find("input:first").val(marker_name).keyup()
+ $("#qtl_results_filter").find("input:first").val(marker_name).keypress()
create_svg: () ->
svg = d3.select("#manhattan_plots")
@@ -279,8 +279,6 @@ $ ->
)
.classed("circle", true)
.on("mouseover", (d) =>
- console.log("foodie")
- console.log("this:", this)
console.log("d3.event is:", d3.event)
console.log("d is:", d)
this_id = "point_" + String(d[2])
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index f5bb0c41..cb3c09cb 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -103,7 +103,7 @@
} else {
marker_name = "";
}
- return $("#qtl_results_filter").find("input:first").val(marker_name).keyup();
+ return $("#qtl_results_filter").find("input:first").val(marker_name).keypress();
};
Manhattan_Plot.prototype.create_svg = function() {
@@ -252,8 +252,6 @@
return "point_" + String(d[2]);
}).classed("circle", true).on("mouseover", function(d) {
var this_id;
- console.log("foodie");
- console.log("this:", _this);
console.log("d3.event is:", d3.event);
console.log("d is:", d);
this_id = "point_" + String(d[2]);
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 46a307b7..09172705 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -8,12 +8,10 @@
<header class="jumbotron subhead" id="overview">
<div class="container">
<h1>GeneNetwork</h1>
- <p class="lead">Open source bioinformatics for systems genetics<br />
- Brought to you by the University of Tennessee</p>
+ <p class="lead">Open source bioinformatics for systems genetics</p>
</div>
</header>
-
<div class="container">
<div class="row">
<div class="span3 bs-docs-sidebar">
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-20 21:56:10 +0000