Fix LDA file name bug

cbg-ethz · Aug 9, 2019 · 5a8d54a · 5a8d54a
1 parent 28613cf
commit 5a8d54a
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/pybda/config/rule_node.py b/pybda/config/rule_node.py
@@ -32,7 +32,7 @@ def __init__(self, method, algorithm, parent, infile, outfolder):
         self.__infile = infile if parent is None else parent.outfile
         self.__level = 0 if parent is None else parent.level + 1
         try:
-            infl_suffix = re.match("(?:.+/)?(.+)\.tsv", self.__infile).group(1)
+            infl_suffix = re.match(r"(?:.+/)?(.+)\.tsv", self.__infile).group(1)
             self.__outfile = os.path.join(
               outfolder, algorithm + "_from_{}".format(infl_suffix)) + ".tsv"
         except AttributeError or TypeError:

diff --git a/pybda/pybda.snake b/pybda/pybda.snake
@@ -168,18 +168,18 @@ rule ica:
 
 rule lda:
     input:
-        expand("{infile}", infile=pybda_config[INFILE__])
+        expand("{infile}", infile=pybda_config.infiles(LDA__))
     output:
         expand("{outfolder}/{dimred}{fls}",
                outfolder=pybda_config[OUTFOLDER__],
-               dimred=LDA__, fls=[".tsv",  "-projection.tsv"]),
+               dimred=pybda_config.outfiles_basename(LDA__),
+               fls=[".tsv",  "-projection.tsv"]),
         directory(expand("{outfolder}/{dimred}-plot",
                          outfolder=pybda_config[OUTFOLDER__],
-                         dimred=LDA__))
+                         dimred=pybda_config.outfiles_basename(LDA__)))
     params:
-        out = expand("{outfolder}/{dimred}",
-                     outfolder=pybda_config[OUTFOLDER__],
-                     dimred=LDA__),
+        out = os.path.join(pybda_config[OUTFOLDER__],
+                           pybda_config.outfiles_basename(LDA__)),
         pca = os.path.join(dirname(), "lda.py"),
         params = " ".join([x for x in pybda_config[SPARKPARAMS__]])
     run:
@@ -192,8 +192,8 @@ rule lda:
             input,
             pybda_config[FEATURES__],
             pybda_config[RESPONSE__],
-            params.out[0],
-            params.out[0] + "-spark.log")
+            params.out,
+            params.out + "-spark.log")
         _run(cmd)