src/obicut.py

@@ -1,5 +1,31 @@
 #!/usr/local/bin/python
+'''
+:py:mod:`obicut`: Trims sequences
+=================================
 
+.. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
+
+:py:mod:`obicut` is a command that trims sequence objects based on two integer 
+values: the ``-b`` option gives the first position of the sequence to be kept, 
+and the ``-e`` option gives the last position to be kept. Both values can be 
+computed using a python expression.
+
+  *Example:*
+    
+    .. code-block:: bash
+        
+          > obicut -b 50 -e seq_length seq1.fasta > seq2.fasta
+    
+    Keeps only the sequence part from the fiftieth position to the end.
+
+  *Example:*
+    
+    .. code-block:: bash
+        
+          > obicut -b 50 -e seq_length-50 seq1.fasta > seq2.fasta
+    
+    Trims the first and last 50 nucleotides of the sequence object.
+'''
 
 from obitools.fasta import fastaIterator,formatFasta
 
@@ -15,8 +41,9 @@ if __name__=='__main__':
     except ImportError:
         pass
 
-    optionParser = getOptionManager([addSequenceFilteringOptions,
+    optionParser = getOptionManager([addSequenceCuttingOptions,
-                                     addSequenceCuttingOptions],
+                                     addSequenceFilteringOptions
+                                     ],
                                     entryIterator=fastaIterator
                                     )