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| author | zsloan | 2018-02-12 19:24:04 +0000 |
|---|---|---|
| committer | zsloan | 2018-02-12 19:24:04 +0000 |
| commit | bfdad191347d037f76c18d246fd7ce7e16af50a8 (patch) | |
| tree | 9ae144de7efc9da5ec0f3e5b244c9d6958cbf83a | |
| parent | ad0e101fd8a0714dea8efa6a5867936f32960e15 (diff) | |
| download | genenetwork2-bfdad191347d037f76c18d246fd7ce7e16af50a8.tar.gz | |
Changed code parsing GEMMA output to fix issue where it wasn't getting the correct p-values
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 18 |
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
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