Merge pull request #455 from CGATOxford/{IS}_py38_errors

Errors picked up by python 3.8's syntax checker
CGATOxford · Feb 5, 2021 · c3ead07 · c3ead07
2 parents a14dea7 + f2e0040
commit c3ead07
Show file tree

Hide file tree

Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/umi_tools/Utilities.py b/umi_tools/Utilities.py
@@ -1175,7 +1175,7 @@ def validateExtractOptions(options):
                                  options.pattern, options.pattern2))
         elif options.extract_method == "regex":
             raise ValueError("barcode regex(es) do not include any umi groups "
-                             "(starting with 'umi_') %s, %s" (
+                             "(starting with 'umi_') %s, %s" % (
                                  options.pattern, options.pattern2))
 
     return(extract_cell, extract_umi)

diff --git a/umi_tools/extract_methods.py b/umi_tools/extract_methods.py
@@ -507,21 +507,21 @@ def __init__(self,
                     raise ValueError("barcode pattern (%s) should only contain "
                                      "N/X/C characters" % pattern)
                 self.pattern_length = len(pattern)
-                self.umi_bases = [x for x in range(len(pattern)) if pattern[x] is "N"]
-                self.bc_bases = [x for x in range(len(pattern)) if pattern[x] is "X"]
-                self.cell_bases = [x for x in range(len(pattern)) if pattern[x] is "C"]
+                self.umi_bases = [x for x in range(len(pattern)) if pattern[x] == "N"]
+                self.bc_bases = [x for x in range(len(pattern)) if pattern[x] == "X"]
+                self.cell_bases = [x for x in range(len(pattern)) if pattern[x] == "C"]
 
             if pattern2:
                 if len(pattern2.replace("N", "").replace("X", "").replace("C", "")) > 0:
                     raise ValueError("barcode pattern2 (%s) should only contain "
                                      "N/X/C characters" % pattern2)
                 self.pattern_length2 = len(pattern2)
                 self.umi_bases2 = [x for x in range(len(pattern2))
-                                   if pattern2[x] is "N"]
+                                   if pattern2[x] == "N"]
                 self.bc_bases2 = [x for x in range(len(pattern2))
-                                  if pattern2[x] is "X"]
+                                  if pattern2[x] == "X"]
                 self.cell_bases2 = [x for x in range(len(pattern2))
-                                    if pattern2[x] is "C"]
+                                    if pattern2[x] == "C"]
 
             self.getCellBarcode = self._getCellBarcodeString
             self.getBarcodes = self._getBarcodesString

diff --git a/umi_tools/whitelist.py b/umi_tools/whitelist.py
@@ -348,7 +348,7 @@ def main(argv=None):
                         options.pattern, options.pattern2))
         elif options.extract_method == "regex":
             U.error("barcode regex(es) do not include any cell groups "
-                    "(starting with 'cell_') %s, %s" (
+                    "(starting with 'cell_') %s, %s" % (
                         options.pattern, options.pattern2))
 
     read1s = umi_methods.fastqIterate(options.stdin)