Merge pull request #223 from PNNL-CompBio/dev

hopefully the last fix for the cptac data modules
PNNL-CompBio · Sep 15, 2023 · 67b152a · 67b152a
2 parents ffd9728 + a2a6b3a
commit 67b152a
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/mRNAData/mRNADataSetsCLI.py b/mRNAData/mRNADataSetsCLI.py
@@ -33,7 +33,7 @@ def main():
         dat = cptac.Luad()
     elif opts.type.lower() == 'ovarian':
         dat = cptac.Ov()
-    elif opts.type.loewr() == 'pdac':
+    elif opts.type.lower() == 'pdac':
         dat = cptac.Pdac()        
     else:
         exit()
@@ -48,6 +48,8 @@ def main():
     tsource = dat_list['transcriptomics']
     df = dat.get_transcriptomics(tsource[0])
 
+    if df.columns.nlevels == 2:
+        df.columns = df.columns.droplevel(1)
 
     # Get the sample type specific dataframe
     # if opts.sample.lower() != 'all':

diff --git a/protData/getAllDatasets.py b/protData/getAllDatasets.py
@@ -34,7 +34,7 @@ def getCancerObj(cancertype):
     return dat
 
 
-for ds in ['brca', 'ccrcc', 'ucec', 'coad','pdac', 'ovarian', 'luad', 'hnscc', 'gbm','lscc']:
+for ds in ['brca', 'ccrcc', 'ucec', 'coad','pdac', 'ov', 'luad', 'hnscc', 'gbm','lscc']:
     dat=getCancerObj(ds)
 
     #this call changed in recent version

diff --git a/protData/protDataSetsCLI.py b/protData/protDataSetsCLI.py
@@ -33,7 +33,7 @@ def main():
         dat = cptac.Luad()
     elif opts.type.lower() == 'ovarian':
         dat = cptac.Ov()
-    elif opts.type.loewr() == 'pdac':
+    elif opts.type.lower() == 'pdac':
         dat = cptac.Pdac()        
     else:
         exit()
@@ -48,6 +48,8 @@ def main():
     tsource = dat_list['proteomics']
     df = dat.get_proteomics(tsource[0])
 
+    if df.columns.nlevels == 2:
+        df.columns = df.columns.droplevel(1)
 
     # Get the sample type specific dataframe
     # if opts.sample.lower() != 'all':