a couple new features, improvements and debug

genepy/google/gcp.py

@@ -78,7 +78,7 @@ def lsFiles(files, add="", group=50):
         for val in sfiles:
             a += val + " "
         data = subprocess.run(
-            "gsutil -m ls " + add + " '" + a"'", capture_output=True, shell=True
+            "gsutil -m ls " + add + " '" + a + "'", capture_output=True, shell=True
         )
         if data.returncode != 0:
             if "One or more URLs matched no objects" not in str(data.stderr):

genepy/mutations/__init__.py

@@ -141,6 +141,8 @@ def read_comments(f):
                         annot = annot.replace("FUNCOTATION=", "")[1:-1]
                         res.update({name: [] for name in funco_fields})
                         for site in annot.split("],["):
+                            if "]#[" in site:
+                                site = site.split("]#[")[0]
                             site = (
                                 site.replace("_%7C_", " ")
                                 .replace("_%20_", " ")

genepy/utils/helper.py

@@ -55,21 +55,21 @@
 }
 
 
-def fileToList(filename):
+def fileToList(filename, strconv=lambda x: x):
     """
     loads an input file with a\\n b\\n.. into a list [a,b,..]
     """
     with open(filename) as f:
-        return [val[:-1] for val in f.readlines()]
+        return [strconv(val[:-1]) for val in f.readlines()]
 
 
-def listToFile(l, filename):
+def listToFile(l, filename, strconv=lambda x: str(x)):
     """
     loads a list with [a,b,..] into an input file a\\n b\\n..
     """
     with open(filename, "w") as f:
         for item in l:
-            f.write("%s\n" % item)
+            f.write("%s\n" % strconv(item))
 
 
 def dictToFile(d, filename):
@@ -1006,39 +1006,32 @@ def cutLoops(li):
 def removeCoVar(mat, maxcorr=0.95):
     """removeCoVar list columns to remove as they covar with other columns
 
+    just regular linear correlation.
+    It displays a list of genes that have been dropped because their correlation
+    to another gene is above a certain value.
+    It shows a python dictionary {gene_to_be_dropped: gene_it_correlates_to}.
+
     Args:
         mat (array like): the matrix of obs x var
         maxcorr (float, optional): the max correlation above which to drop an observation. Defaults to 0.95.
 
     Returns:
         list(tuples): lists of observations to drop and their covarying observation to keep [(todrop,tokeep),...]
     """
+    mat = mat.T
     loc = np.argwhere(np.corrcoef(mat) >= maxcorr)
     nloc = cutLoops(loc)
 
     drop = []
     sameness = []
     for a, b in nloc:
-        if b in drop:
-            if a not in drop:
-                continue
-            else:
-                drop.append(a)
-                for same in sameness:
-                    if same[0] == b:
-                        sameness.append((a, same[0]))
-                        break
-        else:
-            drop.append(b)
-            if a in drop:
-                for same in sameness:
-                    if same[0] == a:
-                        sameness.append((b, same[0]))
-                        break
-            else:
+        if a not in drop:
+            # we already said to drop b: do nothing here
+            if b not in drop:
+                drop.append(b)
                 sameness.append((b, a))
     if type(mat) is pd.DataFrame:
-        col = mat.columns.tolist()
+        col = mat.index.tolist()
         # replace sameness values with the col values
         res = []
         for (i, j) in sameness: