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authorzsloan2018-02-12 19:24:04 +0000
committerzsloan2018-02-12 19:24:04 +0000
commitbfdad191347d037f76c18d246fd7ce7e16af50a8 (patch)
tree9ae144de7efc9da5ec0f3e5b244c9d6958cbf83a /wqflask
parentad0e101fd8a0714dea8efa6a5867936f32960e15 (diff)
downloadgenenetwork2-bfdad191347d037f76c18d246fd7ce7e16af50a8.tar.gz
Changed code parsing GEMMA output to fix issue where it wasn't getting the correct p-values
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py18
1 files changed, 6 insertions, 12 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 68920130..233a5c76 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -3,7 +3,7 @@ import os, math, string, random, json
from base import webqtlConfig
from base.trait import GeneralTrait
from base.data_set import create_dataset
-from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file
+from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR
import utility.logger
logger = utility.logger.getLogger(__name__ )
@@ -11,7 +11,6 @@ logger = utility.logger.getLogger(__name__ )
def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
"""Generates p-values for each marker using GEMMA"""
- assert_bin(GEMMA_COMMAND);
if this_dataset.group.genofile != None:
genofile_name = this_dataset.group.genofile[:-5]
else:
@@ -193,7 +192,7 @@ def parse_gemma_output(genofile_name):
# if marker['chr'] != previous_chr:
# previous_chr = marker['chr']
marker['Mb'] = float(line.split("\t")[2]) / 1000000
- marker['p_value'] = float(line.split("\t")[10])
+ marker['p_value'] = float(line.split("\t")[11])
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
#marker['lrs_value'] = 0
@@ -203,20 +202,15 @@ def parse_gemma_output(genofile_name):
marker_obs.append(marker)
included_markers.append(line.split("\t")[1])
- p_values.append(float(line.split("\t")[10]))
+ p_values.append(float(line.split("\t")[11]))
return marker_obs
def parse_loco_output(this_dataset, gwa_output_filename):
output_filelist = []
- jsonfn = "{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json"
- assert_file(jsonfn)
- try:
- with open(jsonfn) as data_file:
- data = json.load(data_file)
- except:
- logger.error("Can not parse "+jsonfn)
+ with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file:
+ data = json.load(data_file)
files = data['files']
for file in files:
@@ -253,4 +247,4 @@ def parse_loco_output(this_dataset, gwa_output_filename):
included_markers.append(line.split("\t")[1])
p_values.append(float(line.split("\t")[10]))
- return marker_obs
+ return marker_obs \ No newline at end of file