diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 1 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 13 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 16 |
3 files changed, 17 insertions, 13 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 1ef2bc26..1e66e957 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -82,6 +82,7 @@ assert_writable_dir(GENERATED_TEXT_DIR) # Flat file directories GENODIR = flat_files('genotype')+'/' assert_dir(GENODIR) +assert_dir(GENODIR+'bimbam') # for gemma # JSON genotypes are OBSOLETE JSON_GENODIR = flat_files('genotype/json')+'/' diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 57f97a81..d3113302 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -16,7 +16,7 @@ OVERRIDES = {} def app_set(command_id, value): """Set application wide value""" app.config.setdefault(command_id,value) - value + return value def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in @@ -51,7 +51,7 @@ def get_setting(command_id,guess=None): return None # ---- Check whether environment exists - logger.debug("Looking for "+command_id+"\n") + # print("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": command = OVERRIDES.get(command_id) @@ -63,7 +63,7 @@ def get_setting(command_id,guess=None): if command is None or command == "": # print command raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') - logger.debug("Set "+command_id+"="+str(command)) + # print("Set "+command_id+"="+str(command)) return command def get_setting_bool(id): @@ -253,6 +253,7 @@ JS_GN_PATH = get_setting('JS_GN_PATH') PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command()) GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command()) +assert(GEMMA_COMMAND is not None) PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command()) GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() TEMPDIR = tempdir() # defaults to UNIX TMPDIR @@ -266,7 +267,7 @@ from six import string_types if os.environ.get('WQFLASK_OVERRIDES'): jsonfn = get_setting('WQFLASK_OVERRIDES') - logger.error("WQFLASK_OVERRIDES: %s" % jsonfn) + logger.info("WQFLASK_OVERRIDES: %s" % jsonfn) with open(jsonfn) as data_file: overrides = json.load(data_file) for k in overrides: @@ -278,8 +279,4 @@ if os.environ.get('WQFLASK_OVERRIDES'): logger.debug(OVERRIDES) # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") -# assert_dir(get_setting("JS_BIODALLIANCE")) -# assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js") -# assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js") -# assert_dir(get_setting("JS_TWITTER_POST_FETCHER")) assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index a24e43d4..68920130 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 +from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -11,6 +11,7 @@ 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: @@ -27,7 +28,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco): if i < (len(this_chromosomes) - 1): chr_list_string += this_chromosomes[i+1].name + "," else: - chr_list_string += this_chromosomes[i+1].name + chr_list_string += this_chromosomes[i+1].name if covariates != "": gen_covariates_file(this_dataset, covariates) @@ -209,8 +210,13 @@ def parse_gemma_output(genofile_name): def parse_loco_output(this_dataset, gwa_output_filename): output_filelist = [] - with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file: - data = json.load(data_file) + 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) files = data['files'] for file in files: @@ -247,4 +253,4 @@ 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
\ No newline at end of file + return marker_obs |