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authorzsloan2016-02-24 23:36:12 +0000
committerzsloan2016-02-24 23:36:12 +0000
commitece60a2d25ed71980121ac1c1854c3ab3514f453 (patch)
tree6a7d5bb86c48e654b98cabdbea75d31baffc0d3b /wqflask
parent6d8503e53b48ba2e398ff7950d2a722ffc2b6026 (diff)
downloadgenenetwork2-ece60a2d25ed71980121ac1c1854c3ab3514f453.tar.gz
GEMMA mostly working with gn1 mapping, though there may be some issue with the y scale
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py13
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py9
2 files changed, 14 insertions, 8 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index b1ab780c..997b692d 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,6 +1,9 @@
import os
from base import webqtlConfig
+from utility.tools import gemma_command
+
+GEMMA_PATH,GEMMA_COMMAND = gemma_command()
def run_gemma(this_dataset, samples, vals):
"""Generates p-values for each marker using GEMMA"""
@@ -9,9 +12,11 @@ def run_gemma(this_dataset, samples, vals):
gen_pheno_txt_file(this_dataset, samples, vals)
- os.chdir("{}gemma".format(webqtlConfig.HTMLPATH))
+ os.chdir(GEMMA_PATH)
- gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o output/%s_output' % (this_dataset.group.name,
+ gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/output/%s.cXX.txt -lmm 1 -o %s_output' % (GEMMA_PATH,
+ this_dataset.group.name,
+ GEMMA_PATH,
this_dataset.group.name,
this_dataset.group.name)
print("gemma_command:" + gemma_command)
@@ -25,14 +30,14 @@ def run_gemma(this_dataset, samples, vals):
def gen_pheno_txt_file(this_dataset, samples, vals):
"""Generates phenotype file for GEMMA"""
- with open("{}gemma/{}.fam".format(webqtlConfig.HTMLPATH, this_dataset.group.name), "w") as outfile:
+ with open("{}/{}.fam".format(GEMMA_PATH, this_dataset.group.name), "w") as outfile:
for i, sample in enumerate(samples):
outfile.write(str(sample) + " " + str(sample) + " 0 0 0 " + str(vals[i]) + "\n")
def parse_gemma_output(this_dataset):
included_markers = []
p_values = []
- with open("{}gemma/output/{}_output.assoc.txt".format(webqtlConfig.HTMLPATH, this_dataset.group.name)) as output_file:
+ with open("{}/output/{}_output.assoc.txt".format(GEMMA_PATH, this_dataset.group.name)) as output_file:
for line in output_file:
if line.startswith("chr"):
continue
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index c16c885e..5377201b 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -39,10 +39,11 @@ from utility import helper_functions
from utility import Plot, Bunch
from utility import temp_data
from utility.benchmark import Bench
-from utility.tools import pylmm_command, plink_command
+from utility.tools import pylmm_command, plink_command, gemma_command
PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
PLINK_PATH,PLINK_COMMAND = plink_command()
+GEMMA_PATH,GEMMA_COMMAND = gemma_command()
class MarkerRegression(object):
@@ -86,7 +87,7 @@ class MarkerRegression(object):
self.dataset.group.get_markers()
if self.mapping_method == "gemma":
- self.score_type = "LOD"
+ self.score_type = "LRS"
included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals)
self.dataset.group.get_specified_markers(markers = included_markers)
self.dataset.group.markers.add_pvalues(p_values)
@@ -219,9 +220,9 @@ class MarkerRegression(object):
self.gen_pheno_txt_file()
- os.chdir("/home/zas1024/gene/web/gemma")
+ #os.chdir("/home/zas1024/gene/web/gemma")
- gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % (
+ gemma_command = GEMMA_COMMAND + ' -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % (
self.dataset.group.name,
self.dataset.group.name,
self.dataset.group.name)