updated docs to reflect codon-based trimming option

JLSteenwyk · Feb 6, 2024 · df840eb · df840eb
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diff --git a/change_log.txt b/change_log.txt
@@ -1,5 +1,9 @@
 Major changes to ClipKIT are summarized here.
 
+2.1.2
+Incorporate codon-based trimming. When one position in a codon gets trimmed based on the mode
+being used, the whole codon will get trimmed from the alignment.
+
 2.0.0 through 2.1.0
 Introduce and refactor MSA class. Rely on Numpy functionality to accelerate processes.
 

diff --git a/clipkit/version.py b/clipkit/version.py
@@ -1 +1 @@
-__version__ = "2.1.1"
+__version__ = "2.1.2"
diff --git a/docs/advanced/index.rst b/docs/advanced/index.rst
@@ -115,6 +115,24 @@ Output file with the suffix '.clipkit.complementary'
 
 |
 
+.. _Codon:
+
+Codon
+-----
+
+Trims codon-based alignments. If one position in a codon should be trimmed, the whole
+codon will be trimmed. To conduct codon-based trimming, use the -co/\\-\\-codon argument.
+
+.. code-block:: shell
+
+	clipkit <input> --codon
+
+    # or
+
+	clipkit <input> --co
+
+|
+
 .. _`Sequence Type`:
 
 Sequence Type
@@ -151,23 +169,25 @@ All options
 +-----------------------------+-------------------------------------------------------------------+
 | Option                      | Usage and meaning                                                 |
 +=============================+===================================================================+
-| -h/\\-\\-help                 | Print help message                                                |
+| -h/\\-\\-help               | Print help message                                                |
++-----------------------------+-------------------------------------------------------------------+
+| -v/\\-\\-version            | Print software version                                            |
 +-----------------------------+-------------------------------------------------------------------+
-| -v/\\-\\-version              | Print software version                                            |
+| -m/\\-\\-mode               | Specify trimming mode (default: smart-gap)                        |
 +-----------------------------+-------------------------------------------------------------------+
-| -m/\\-\\-mode                 | Specify trimming mode (default: smart-gap)                        |
+| -o/\\-\\-output             | Specify output file name                                          |
 +-----------------------------+-------------------------------------------------------------------+
-| -o/\\-\\-output               | Specify output file name                                          |
+| -g/\\-\\-gaps               | Specify gappyness threshold (between 0 and 1). *Default: 0.9*     |
 +-----------------------------+-------------------------------------------------------------------+
-| -g/\\-\\-gaps                 | Specify gappyness threshold (between 0 and 1). *Default: 0.9*     |
+| -co/\\-\\-codon             | Codon codon-based trimming. *Default: off*                        |
 +-----------------------------+-------------------------------------------------------------------+
-| -if/\\-\\-input_file_format   | Specify input file format*. *Default: auto-detect*                |
+| -if/\\-\\-input_file_format | Specify input file format*. *Default: auto-detect*                |
 +-----------------------------+-------------------------------------------------------------------+
-| -of/\\-\\-output_file_format  | Specify output file format*. *Default: input file type*           |
+| -of/\\-\\-output_file_format| Specify output file format*. *Default: input file type*           |
 +-----------------------------+-------------------------------------------------------------------+
-| -l/\\-\\-log                  | Create a log file. *Default: off*                                 |
+| -l/\\-\\-log                | Create a log file. *Default: off*                                 |
 +-----------------------------+-------------------------------------------------------------------+
-| -c/\\-\\-complementary          | Create a complementary alignment file. *Default: off*             |
+| -c/\\-\\-complementary      | Create a complementary alignment file. *Default: off*             |
 +-----------------------------+-------------------------------------------------------------------+
 
 

diff --git a/docs/change_log/index.rst b/docs/change_log/index.rst
@@ -8,6 +8,10 @@ Change log
 
 Major changes to ClipKIT are summarized here.
 
+**2.1.2**
+Incorporate codon-based trimming. When one position in a codon gets trimmed based on the mode
+being used, the whole codon will get trimmed from the alignment.
+
 **1.4.0**
 new argument for specifying if sequences are amino acids or nucleotides