Skip to content

Commit

Permalink
added cst mode to the docs
Browse files Browse the repository at this point in the history
  • Loading branch information
@JLSteenwyk
JLSteenwyk committed Mar 18, 2024
1 parent 5c0db77 commit d15729c
Showing 1 changed file with 91 additions and 27 deletions.
118 changes: 91 additions & 27 deletions docs/advanced/index.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ This section describes the various features and options of ClipKIT.
- Log_
- Complementary_
- Codon_
- `Custom site trimming (cst mode)`_
- Gaps_
- `Gap Characters`_
- `Sequence Type`_
Expand Down Expand Up @@ -37,6 +38,7 @@ ClipKIT can be run with eight different modes, which are specified with the -m/-
* kpi-smart-gap: a combination of kpi- and smart-gap-based trimming
* kpi-gappy: a combination of kpi- and gappy-based trimming
* c3: remove third codon position from alignment
* cst: custom site trimming (remove sites specified by the user)

.. code-block:: shell
Expand Down Expand Up @@ -68,6 +70,9 @@ ClipKIT can be run with eight different modes, which are specified with the -m/-
# remove third codon position
clipkit <input> -m c3
# conduct site-specific trimming
clipkit <input> -m cst -a <auxiliary file>
.. _Output:

|
Expand Down Expand Up @@ -140,6 +145,63 @@ codon will be trimmed. To conduct codon-based trimming, use the -co/\\-\\-codon
|

.. _`Custom site trimming (cst mode)`:

Custom site trimming (cst mode)
-------------------------------

Custom site trimming specified using a tab-delimited text file specified using the -a argument.

.. code-block:: shell
clipkit <input> -m cst -a <auxiliary_file>
|
The `auxiliary_file` is a two column tab-delimited file wherein the first column is the site
(starting at 1) and the second column specifies if the site should be kept or trimmed using the
strings "keep" or "trim".

.. code-block:: shell
cat auxiliary_file.txt
1 keep
2 trim
3 keep
4 keep
5 keep
6 keep
|
Alternatively, users can specify sites that are only kept or trimmed using the `auxiliary_file`.
For example, the following would be equivalent to the auxiliary file described above.

.. code-block:: shell
cat auxiliary_file.txt
2 trim
|
Similarly, the following would conduct the trimming, wherein the second site is removed but all
others are kept.

.. code-block:: shell
cat auxiliary_file.txt
1 keep
3 keep
4 keep
5 keep
6 keep
|
.. _Gaps:

Gaps
Expand Down Expand Up @@ -211,33 +273,35 @@ All options
---------------------


+-----------------------------+-----------------------------------------------------------------------+
| Option | Usage and meaning |
+=============================+=======================================================================+
| -h/\\-\\-help | Print help message |
+-----------------------------+-----------------------------------------------------------------------+
| -v/\\-\\-version | Print software version |
+-----------------------------+-----------------------------------------------------------------------+
| -m/\\-\\-mode | Specify trimming mode (default: smart-gap) |
+-----------------------------+-----------------------------------------------------------------------+
| -o/\\-\\-output | Specify output file name |
+-----------------------------+-----------------------------------------------------------------------+
| -g/\\-\\-gaps | Specify gappyness threshold (between 0 and 1). *Default: 0.9* |
+-----------------------------+-----------------------------------------------------------------------+
| -gc/\\-\\-gap_characters | Specifies gap characters used in input file (AAs: Xx-?*; NTs: XxNn-?* |
+-----------------------------+-----------------------------------------------------------------------+
| -co/\\-\\-codon | Codon codon-based trimming. *Default: off* |
+-----------------------------+-----------------------------------------------------------------------+
| -s/\\-\\-sequence | Specifies sequence type of input file. *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* |
+-----------------------------+-----------------------------------------------------------------------+
| -l/\\-\\-log | Create a log file. *Default: off* |
+-----------------------------+-----------------------------------------------------------------------+
| -c/\\-\\-complementary | Create a complementary alignment file. *Default: off* |
+-----------------------------+-----------------------------------------------------------------------+
+-----------------------------+-------------------------------------------------------------------------+
| Option | Usage and meaning |
+=============================+=========================================================================+
| -h/\\-\\-help | Print help message |
+-----------------------------+-------------------------------------------------------------------------+
| -v/\\-\\-version | Print software version |
+-----------------------------+-------------------------------------------------------------------------+
| -m/\\-\\-mode | Specify trimming mode (default: smart-gap) |
+-----------------------------+-------------------------------------------------------------------------+
| -o/\\-\\-output | Specify output file name |
+-----------------------------+-------------------------------------------------------------------------+
| -g/\\-\\-gaps | Specify gappyness threshold (between 0 and 1). *Default: 0.9* |
+-----------------------------+-------------------------------------------------------------------------+
| -gc/\\-\\-gap_characters | Specifies gap characters used in input file (AAs: Xx-?*; NTs: XxNn-?* |
+-----------------------------+-------------------------------------------------------------------------+
| -co/\\-\\-codon | Codon codon-based trimming. *Default: off* |
+-----------------------------+-------------------------------------------------------------------------+
| -s/\\-\\-sequence | Specifies sequence type of input file. *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* |
+-----------------------------+-------------------------------------------------------------------------+
| -l/\\-\\-log | Create a log file. *Default: off* |
+-----------------------------+-------------------------------------------------------------------------+
| -c/\\-\\-complementary | Create a complementary alignment file. *Default: off* |
+-----------------------------+-------------------------------------------------------------------------+
| -a/\\-\\-auxiliary_file | Auxiliary file. Currently used for specifying sites to trim in cst mode |
+-----------------------------+-------------------------------------------------------------------------+


\*Acceptable file formats include:
Expand Down

0 comments on commit d15729c

Please sign in to comment.