doc

src/illuminapairedend.py

@@ -5,7 +5,9 @@
 
 .. codeauthor:: Eric Coissac <eric.coissac@metabarcoding.org>
 
-.. IMPORTANT:: :py:mod:`illuminapairedend` replaces ``solexapairend``.
+.. IMPORTANT::
+
+  :py:mod:`illuminapairedend` replaces ``solexapairend``.
 
 :py:mod:`illuminapairedend` aims at aligning the two reads of a pair-end library sequenced 
 using an Illumina platform. 

src/obitools/options/bioseqedittag.py

@@ -111,14 +111,14 @@ def addSequenceEditTagOptions(optionManager):
                              dest='taxonrank',
                              default=[],
                              type="string",
-                             help="add taxonomy annotation at a speciefied rank level")
+                             help="add taxonomy annotation at a specified rank level")
     
     group.add_option('-m','--mcl',
                              action="store", dest="mcl",
                              metavar="<mclfile>",
                              type="string",
                              default=None,
-                             help="split following mcl graph clustering partition")
+                             help="add cluster tag to sequences according to a mcl graph clustering partition")
     
     group.add_option('--uniq-id',
                              action="store_true", dest="uniqids",

src/obiuniq.py

@@ -66,7 +66,7 @@ def addUniqOptions(optionManager):
     group.add_option('-i','--merge-ids',
                              action="store_true", dest="mergeids",
                              default=False,
-                             help="Add the merged id data to output")
+                             help="Add the merged key with all ids of merged sequences")
    
     group.add_option('-c','--category-attribute',
                              action="append", dest="categories",