Merge pull request #176 from PNNL-CompBio/copy-fix

added fix for copy number

Author: sgosline

build/broad_sanger/02-broadSangerOmics.R

@@ -105,6 +105,15 @@ sanger_files<-function(fi,value){
        rm(exp_file)
 
         print('copy call')
+
+        ##rename SANGER value
+        # Amplification -> amp
+        # Deletion -> deep del
+        # Loss -> het loss
+        # Gain -> gain
+        # Neutral -> diploid
+        #
+        res$Sanger=sapply(res$Sanger,function(x) ifelse(x=='Amplification','amp',ifelse(x=='Deletion','deep del',ifelse(x=='Loss','het loss',ifelse(x=='Gain','gain','diploid')))))
       ##calibrate the copy call
       res<-res|> ##deep del < 0.5210507 < het loss < 0.7311832 < diploid < 1.214125 < gain < 1.422233 < amp
         dplyr::mutate(IMPROVE=ifelse(copy_number<0.5210507,'deep del',

build/build_all.py

@@ -103,7 +103,7 @@ def main():
 
             if not os.path.exists('local/'+da+'_drugs.tsv'):
                 run_cmd([di,'sh','build_drugs.sh',','.join(dflist)],da+' drugs')
-            dflist = dflist.append('/tmp/'+da+'_drugs.tsv')
+            dflist.append('/tmp/'+da+'_drugs.tsv')
 
     #### Any new omics files are created here.
     ## depends on samples!
@@ -127,7 +127,7 @@ def main():
             else:
                 di = da
             if not os.path.exists('local/'+da+'_experiments.tsv'):
-                run_cmd([di,'sh','build_exp.sh','/tmp/'+df+'_samples.csv','/tmp/'+da+'_drugs.tsv'],da+' experiments')
+                run_cmd([di,'sh','build_exp.sh','/tmp/'+da+'_samples.csv','/tmp/'+da+'_drugs.tsv'],da+' experiments')