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| author | Pjotr Prins | 2016-04-20 08:51:57 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2016-04-20 08:51:57 +0000 |
| commit | 1675f34eeff84d7ec0f43c1676f9107e202dda88 (patch) | |
| tree | 7640f085774eb774d49b463f54d4251be6ad4d75 | |
| parent | 3be9e4a0950b1ea2d560463032c6f4104baf738e (diff) | |
| download | genenetwork2-1675f34eeff84d7ec0f43c1676f9107e202dda88.tar.gz | |
[PATCH 027/100] Introduce tools.locate
| -rw-r--r-- | wqflask/utility/tools.py | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 5 |
2 files changed, 15 insertions, 4 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 5d69e699..624df179 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -78,11 +78,23 @@ def flat_files(subdir=None): return valid_path(base+"/"+subdir) return valid_path(base) +def locate(name, subdir=None): + base = get_setting("GENENETWORK_FILES") + if subdir: + base = base+"/"+subdir + if valid_path(base): + lookfor = base + "/" + name + if valid_path(lookfor): + return lookfor + else: + raise IOError("Can not locate "+lookfor) + raise IOError("Can not locate "+name) + def tempdir(): return valid_path(get_setting("TEMPDIR","/tmp")) + # Cached values - PYLMM_COMMAND = pylmm_command() GEMMA_COMMAND = pylmm_command() PLINK_COMMAND = pylmm_command() diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index a76a5967..36334317 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -41,7 +41,7 @@ from wqflask.marker_regression import gemma_mapping #from wqflask.marker_regression import plink_mapping #from wqflask.marker_regression import rqtl_mapping -from utility.tools import PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND +from utility.tools import locate, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND class MarkerRegression(object): @@ -979,8 +979,7 @@ class MarkerRegression(object): #def gen_human_results(self, pheno_vector, tempdata): def gen_human_results(self, pheno_vector, key, temp_uuid): - file_base = os.path.join(webqtlConfig.PYLMM_PATH, self.dataset.group.name) - print("file_base:", file_base) + file_base = locate(self.dataset.group.name,"mapping") plink_input = input.plink(file_base, type='b') input_file_name = os.path.join(webqtlConfig.SNP_PATH, self.dataset.group.name + ".snps.gz") |