diff options
| -rwxr-xr-x | wqflask/base/webqtlConfig.py | 6 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/MarkerRegressionPage.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 2 |
3 files changed, 6 insertions, 6 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 6890dacf..0358bcbf 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -56,9 +56,9 @@ UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit" ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s" -# HTMLPATH = GNROOT + 'genotype_files/' -# PYLMM_PATH -# IMGDIR = GNROOT + '/wqflask/wqflask/static/output/' +# The following paths are no longer in use! +# HTMLPATH is replaced by GENODIR +# IMGDIR is replaced by GENERATED_IMAGE_DIR # Temporary storage: TMPDIR = mk_dir(TEMPDIR+'/gn2/') diff --git a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py index 455fcf95..4c3391e5 100755 --- a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py +++ b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py @@ -72,7 +72,7 @@ class MarkerRegressionPage(templatePage): #automatically generate pheno txt file for PLINK self.genPhenoTxtFileForPlink(phenoFileName=plinkOutputFileName,RISetName=fd.RISet,probesetName=probesetName, valueDict=allTraitValueDict) # os.system full path is required for input and output files; specify missing value is -9999 - plink_command = '%splink/plink --noweb --ped %splink/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %splink/%s.map --pheno %s/%s.txt --pheno-name %s --missing-phenotype -9999 --out %s%s --assoc ' % (webqtlConfig.HTMLPATH, webqtlConfig.HTMLPATH, fd.RISet, webqtlConfig.HTMLPATH, fd.RISet, webqtlConfig.TMPDIR, plinkOutputFileName, probesetName, webqtlConfig.TMPDIR, plinkOutputFileName) + plink_command = '%splink/plink --noweb --ped %splink/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %splink/%s.map --pheno %s/%s.txt --pheno-name %s --missing-phenotype -9999 --out %s%s --assoc ' % (webqtlConfig.GENODIR, webqtlConfig.GENODIR, fd.RISet, webqtlConfig.GENODIR, fd.RISet, webqtlConfig.TMPDIR, plinkOutputFileName, probesetName, webqtlConfig.TMPDIR, plinkOutputFileName) os.system(plink_command) @@ -1597,7 +1597,7 @@ class MarkerRegressionPage(templatePage): # get strain name from ped file in order def getStrainNameFromPedFile(self, RISetName=''): - pedFileopen= open("%splink/%s.ped"%(webqtlConfig.HTMLPATH, RISetName),"r") + pedFileopen= open("%splink/%s.ped"%(webqtlConfig.GENODIR, RISetName),"r") line =pedFileopen.readline() strainNameList=[] diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 8fb086c1..caea5802 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -11,7 +11,7 @@ def run_gemma(this_dataset, samples, vals): gen_pheno_txt_file(this_dataset, samples, vals) # Don't do this! - # os.chdir("{}gemma".format(webqtlConfig.HTMLPATH)) + # os.chdir("{}gemma".format(webqtlConfig.GENODIR)) # use GEMMA_RUN in the next one, create a unique temp file |