Ac tables2table

cgat/tools/tables2table.py

@@ -280,15 +280,20 @@ def main(argv=sys.argv):
 
     E.info("combining %i tables" % len(args.filenames))
 
-    if args.cat:
-        table = concatenate_tables(args.filenames,
-                                   regex_filename=args.regex_filename,
-                                   separator=args.separator,
-                                   headers=args.headers,
-                                   missing_value=args.missing_value,
-                                   cat=args.cat)
-
-    table.to_csv(args.stdout, sep=args.separator, index=False)
+    # Remove the if statement and call concatenate_tables directly
+    table = concatenate_tables(args.filenames,
+                               regex_filename=args.regex_filename,
+                               separator=args.separator,
+                               headers=args.headers,
+                               missing_value=args.missing_value,
+                               cat=args.cat)
+
+    # Ensure the table object is not None before attempting to write it
+    if table is not None:
+        table.to_csv(args.stdout, sep=args.separator, index=False)
+    else:
+        E.warn("No tables were concatenated.")
+
     E.stop()
 
 

conda/environments/cgat-apps.yml

@@ -23,7 +23,7 @@ dependencies:
 - pep8
 - pybedtools
 - pybigwig
-- pysam>=0.18.0
+- pysam
 - pyyaml
 - quicksect
 - rdflib