diff mutation_column_checker.py @ 83:729738462297 draft

"planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"

--- a/mutation_column_checker.py	Thu Feb 25 10:32:32 2021 +0000
+++ b/mutation_column_checker.py	Wed Sep 15 12:24:06 2021 +0000
@@ -1,27 +1,27 @@
-import re
-
-mutationMatcher = re.compile("^([nactg])(\d+).([nactg]),?[ ]?([A-Z])?(\d+)?[>]?([A-Z;])?(.*)?")
-
-with open("7_V-REGION-mutation-and-AA-change-table.txt", 'r') as file_handle:
-    first = True
-    fr3_index = -1
-    for i, line in enumerate(file_handle):
-        line_split = line.split("\t")
-        if first:
-            fr3_index = line_split.index("FR3-IMGT")
-            first = False
-            continue
-
-        if len(line_split) < fr3_index:
-            continue
-        
-        fr3_data = line_split[fr3_index]
-        if len(fr3_data) > 5:
-            try:
-                test = [mutationMatcher.match(x).groups() for x in fr3_data.split("|") if x]
-            except:
-                print(line_split[1])
-                print("Something went wrong at line {line} with:".format(line=line_split[0]))
-                #print([x for x in fr3_data.split("|") if not mutationMatcher.match(x)])
-        if i % 100000 == 0:
-            print(i)
+import re
+
+mutationMatcher = re.compile("^([nactg])(\d+).([nactg]),?[ ]?([A-Z])?(\d+)?[>]?([A-Z;])?(.*)?")
+
+with open("7_V-REGION-mutation-and-AA-change-table.txt", 'r') as file_handle:
+    first = True
+    fr3_index = -1
+    for i, line in enumerate(file_handle):
+        line_split = line.split("\t")
+        if first:
+            fr3_index = line_split.index("FR3-IMGT")
+            first = False
+            continue
+
+        if len(line_split) < fr3_index:
+            continue
+        
+        fr3_data = line_split[fr3_index]
+        if len(fr3_data) > 5:
+            try:
+                test = [mutationMatcher.match(x).groups() for x in fr3_data.split("|") if x]
+            except:
+                print((line_split[1]))
+                print(("Something went wrong at line {line} with:".format(line=line_split[0])))
+                #print([x for x in fr3_data.split("|") if not mutationMatcher.match(x)])
+        if i % 100000 == 0:
+            print(i)