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-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py14
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py37
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.coffee2
-rw-r--r--wqflask/wqflask/static/new/javascript/marker_regression.js2
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee6
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js7
-rw-r--r--wqflask/wqflask/views.py2
7 files changed, 53 insertions, 17 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index f67c595a..5f4f9be8 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -9,6 +9,7 @@ import string
import sys
import os
import collections
+import pdb
import numpy as np
from scipy import linalg
@@ -67,13 +68,13 @@ class MarkerRegression(object):
pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
if self.dataset.group.species == "human":
- p_values, t_stats = self.gen_human_results(pheno_vector)
+ p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
else:
genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
no_val_samples = self.identify_empty_samples()
- trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
-
+ trimmed_genotype_data = self.trim_genotypes(genotype_data, no_value_samples=[])
+ pdb.set_trace()
genotype_matrix = np.array(trimmed_genotype_data).T
print("pheno_vector is: ", pf(pheno_vector))
@@ -92,10 +93,12 @@ class MarkerRegression(object):
self.qtl_results = self.dataset.group.markers.markers
- def gen_human_results(self, pheno_vector):
+ def gen_human_results(self, pheno_vector, tempdata):
file_base = os.path.join(webqtlConfig.PYLMM_PATH, self.dataset.group.name)
+ tempdata.store("percent_complete", 0)
plink_input = input.plink(file_base, type='b')
+ tempdata.store("percent_complete", 0.1)
pheno_vector = pheno_vector.reshape((len(pheno_vector), 1))
covariate_matrix = np.ones((pheno_vector.shape[0],1))
@@ -106,7 +109,8 @@ class MarkerRegression(object):
pheno_vector,
covariate_matrix,
plink_input,
- kinship_matrix
+ kinship_matrix,
+ temp_data=tempdata
)
return p_values, t_stats
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index e60f7b02..4de77173 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -23,6 +23,7 @@ import numpy as np
from scipy import linalg
from scipy import optimize
from scipy import stats
+import pdb
from pprint import pformat as pf
@@ -43,10 +44,10 @@ def run_human(pheno_vector,
if v.sum():
pheno_vector = pheno_vector[keep]
- print("pheno_vector shape is now: ", pf(pheno_vector.shape))
+ #print("pheno_vector shape is now: ", pf(pheno_vector.shape))
covariate_matrix = covariate_matrix[keep,:]
- print("kinship_matrix shape is: ", pf(kinship_matrix.shape))
- print("len(keep) is: ", pf(keep.shape))
+ #print("kinship_matrix shape is: ", pf(kinship_matrix.shape))
+ #print("len(keep) is: ", pf(keep.shape))
kinship_matrix = kinship_matrix[keep,:][:,keep]
n = kinship_matrix.shape[0]
@@ -58,13 +59,21 @@ def run_human(pheno_vector,
# Buffers for pvalues and t-stats
p_values = []
t_stats = []
+
+ plink_input.getSNPIterator()
+ total_snps = plink_input.numSNPs
+
count = 0
with Bench("snp iterator loop"):
for snp, this_id in plink_input:
- if count > 1000:
- break
+ #if count > 1000:
+ # break
count += 1
+ percent_complete = (float(count) / total_snps) * 100
+ print("percent_complete: ", pf(percent_complete))
+ temp_data.store("percent_complete", percent_complete)
+
x = snp[keep].reshape((n,1))
#x[[1,50,100,200,3000],:] = np.nan
v = np.isnan(x).reshape((-1,))
@@ -104,9 +113,12 @@ def run_human(pheno_vector,
if refit:
lmm_ob.fit(X=x)
ts, ps, beta, betaVar = lmm_ob.association(x)
+
p_values.append(ps)
t_stats.append(ts)
+ print("p_values: ", pf(p_values))
+
return p_values, t_stats
@@ -188,14 +200,13 @@ def calculate_kinship(genotype_matrix, temp_data):
#print("m is:", m)
keep = []
for counter in range(m):
- print("type of genotype_matrix[:,counter]:", pf(genotype_matrix[:,counter]))
+ #print("type of genotype_matrix[:,counter]:", pf(genotype_matrix[:,counter]))
#Checks if any values in column are not numbers
not_number = np.isnan(genotype_matrix[:,counter])
- print("type of not_number:", type(not_number))
#Gets vector of values for column (no values in vector if not all values in col are numbers)
marker_values = genotype_matrix[True - not_number, counter]
- print("type of marker_values is:", type(marker_values))
+ #print("type of marker_values is:", type(marker_values))
#Gets mean of values in vector
values_mean = marker_values.mean()
@@ -270,7 +281,10 @@ def GWAS(pheno_vector,
p_values = []
t_statistics = []
-
+
+ n = genotype_matrix.shape[0]
+ m = genotype_matrix.shape[1]
+
for counter in range(m):
x = genotype_matrix[:,counter].reshape((n, 1))
v = np.isnan(x).reshape((-1,))
@@ -343,6 +357,7 @@ class LMM:
#x = Y != -9
x = True - np.isnan(Y)
+ #pdb.set_trace()
if not x.sum() == len(Y):
if self.verbose: sys.stderr.write("Removing %d missing values from Y\n" % ((True - x).sum()))
Y = Y[x]
@@ -362,8 +377,8 @@ 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))
+ #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/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 3e14ab6b..78b6fdbc 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -4,10 +4,12 @@ $ ->
@qtl_results = js_data.qtl_results
console.log("qtl_results are:", @qtl_results)
@chromosomes = js_data.chromosomes
+ console.log("chromosomes: ", @chromosomes)
@total_length = 0
@max_chr = @get_max_chr()
+ console.log("max_chr is: ", @max_chr)
@x_coords = []
@y_coords = []
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index 09470daf..25d88ec0 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -13,8 +13,10 @@
this.qtl_results = js_data.qtl_results;
console.log("qtl_results are:", this.qtl_results);
this.chromosomes = js_data.chromosomes;
+ console.log("chromosomes: ", this.chromosomes);
this.total_length = 0;
this.max_chr = this.get_max_chr();
+ console.log("max_chr is: ", this.max_chr);
this.x_coords = [];
this.y_coords = [];
this.marker_names = [];
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 157f56a9..22427e4f 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -37,6 +37,12 @@ $ ->
type: "POST"
url: url
data: form_data
+ error: (xhr, ajaxOptions, thrownError) =>
+ alert("some error occurred")
+ console.log(xhr)
+ clearInterval(this.my_timer)
+ $('#progress_bar_container').modal('hide')
+ $("body").html("error")
success: (data) =>
clearInterval(this.my_timer)
$('#progress_bar_container').modal('hide')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 78459692..daf9b273 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -46,6 +46,13 @@
type: "POST",
url: url,
data: form_data,
+ error: function(xhr, ajaxOptions, thrownError) {
+ alert("some error occurred");
+ console.log(xhr);
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ return $("body").html("error");
+ },
success: function(data) {
clearInterval(_this.my_timer);
$('#progress_bar_container').modal('hide');
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 7f5f88e0..c303e0d1 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -168,7 +168,7 @@ def marker_regression_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- version = "v13"
+ version = "v14"
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
with Bench("Loading cache"):
result = Redis.get(key)