diff spring_cross.py @ 38:80a4b98121b6 draft

"planemo upload commit 22cd6b0fa88ce0ddc4052beab306f5ba10754f12"

--- a/spring_cross.py	Wed Nov 25 14:35:35 2020 +0000
+++ b/spring_cross.py	Wed Nov 25 17:38:24 2020 +0000
@@ -7,7 +7,9 @@
 
 
 def getId(line):
-    line = line.split()[0]
+    line = line.strip()
+    if len(line) != 6 or line[4:5] != "_":
+        raise Exception("Invalid list entry (`PDB_CHAIN`): %s." % line)
     return line[:4].upper() + line[4:6]
 
 
@@ -61,8 +63,8 @@
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description='List filtering.')
     parser.add_argument('-l', '--list', help='List of PDB chains [PDB_CHAIN]', required=True)
-    parser.add_argument('-i', '--index', help='PDB Database Index file (dbkit_index)', required=True)
-    parser.add_argument('-d', '--database', help='PDB Database files (dbkit)', required=True)
+    parser.add_argument('-i', '--index', help='PDB Database Index file (ffindex)', required=True)
+    parser.add_argument('-d', '--database', help='PDB Database files (ffdata)', required=True)
     parser.add_argument('-o', '--output', help='Output file', required=True)
     parser.add_argument('-t', '--temp', help='Temporary Directory', required=True)
     parser.add_argument('-g', '--log', help='Log File', required=True)