Altered if clasuses around selection of commands in umi_tools.py

umi_tools/count.py

@@ -75,6 +75,10 @@ def main(argv=None):
     parser = U.OptionParser(version="%prog version: $Id$",
                             usage=usage,
                             description=globals()["__doc__"])
+    if len(argv) == 1:
+        parser.print_usage()
+        print ("Required options missing, see --help for more details")
+        return 1
 
     group = U.OptionGroup(parser, "count-specific options")
 

umi_tools/count_tab.py

@@ -92,6 +92,11 @@ def main(argv=None):
                             usage=usage,
                             description=globals()["__doc__"])
 
+    if len(argv) == 1:
+        parser.print_usage()
+        print ("Required options missing, see --help for more details")
+        return 1
+
     group = U.OptionGroup(parser, "count_tab-specific options")
 
     group.add_option("--barcode-separator", dest="bc_sep",

umi_tools/dedup.py

@@ -187,6 +187,11 @@ def main(argv=None):
     parser = U.OptionParser(version="%prog version: $Id$",
                             usage=usage,
                             description=globals()["__doc__"])
+    if len(argv) == 1:
+        parser.print_usage()
+        print ("Required options missing, see --help for more details")
+        return 1
+
     group = U.OptionGroup(parser, "dedup-specific options")
 
     group.add_option("--output-stats", dest="stats", type="string",

umi_tools/extract.py

@@ -186,6 +186,11 @@ def main(argv=None):
                             usage=usage,
                             description=globals()["__doc__"])
 
+    if len(argv) == 1:
+        parser.print_usage()
+        print ("Required options missing, see --help for more details")
+        return 1
+
     group = U.OptionGroup(parser, "extract-specific options")
 
     # (Experimental option) Retain the UMI in the sequence read"

umi_tools/group.py

@@ -127,6 +127,11 @@ def main(argv=None):
                             usage=usage,
                             description=globals()["__doc__"])
 
+    if len(argv) == 1:
+        parser.print_usage()
+        print ("Required options missing, see --help for more details")
+        return 1
+
     group = U.OptionGroup(parser, "group-specific options")
 
     group.add_option("--group-out", dest="tsv", type="string",

umi_tools/umi_tools.py

@@ -1,10 +1,8 @@
 '''
 umi_tools.py - Tools for UMI analyses
-===============================================
+=====================================
 
 :Author: Tom Smith & Ian Sudbury, CGAT
-:Release: $Id$
-:Date: |today|
 :Tags: Genomics UMI
 
 There are 6 tools:
@@ -50,12 +48,22 @@ def main(argv=None):
 
         return
 
-    elif argv[2] in ["--help", "-h", "--help-extended"]:
+    elif len(argv) > 2 and  argv[2] in ["--help", "-h", "--help-extended"]:
         print("UMI-Tools: Version %s" % __version__)
 
     command = argv[1]
 
-    module = importlib.import_module("umi_tools." + command, "umi_tools")
+    try:
+        module = importlib.import_module("umi_tools." + command, "umi_tools")
+    except ImportError:
+        print("Command %s not recognosied" % command)
+        print()
+        print("For full UMI-tools documentation, see: "
+              "https://umi-tools.readthedocs.io/en/latest/\n")
+        print(globals()["__doc__"])
+
+        return (1)
+
     # remove 'umi-tools' from sys.argv
     del sys.argv[0]
     module.main(sys.argv)

umi_tools/whitelist.py

@@ -249,6 +249,10 @@ def main(argv=None):
     parser = U.OptionParser(version="%prog version: $Id$",
                             usage=usage,
                             description=globals()["__doc__"])
+    if len(argv) == 1:
+        parser.print_usage()
+        print ("Required options missing, see --help for more details")
+        return 1
 
     group = U.OptionGroup(parser, "whitelist-specific options")