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@JLSteenwyk
JLSteenwyk committed Mar 6, 2024
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90 changes: 67 additions & 23 deletions _sources/advanced/index.rst.txt
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Expand Up @@ -10,6 +10,8 @@ This section describes the various features and options of ClipKIT.
- Log_
- Complementary_
- Codon_
- Gaps_
- `Gap Characters`_
- `Sequence Type`_
- `All options`_

Expand Down Expand Up @@ -138,6 +140,44 @@ codon will be trimmed. To conduct codon-based trimming, use the -co/\\-\\-codon
|
.. _Gaps:

Gaps
----

Positions with gappyness greater than threshold will be trimmed.
Must be between 0 and 1. (Default: 0.9). This argument is ignored
when using the kpi and kpic mdoes of trimming as well as an
iteration of trimming that uses smart-gap.

To specify a gaps threshold, use the -g/\\-\\-gaps argument.

.. code-block:: shell
clipkit <input> --gaps 0.4
# or
clipkit <input> --g 0.4
|
.. _`Gap Characters`:

Gap Characters
--------------

Specifies gap characters used in the input file. For example,
"NnXx-?" would specify that "N", "n", "X", "x", "-", and "?" are
gap characters. Note, the first gap character cannot be "-" because
the parser will interpret the gaps list as a new argument.

.. code-block:: shell
clipkit <input> -gc NnXx-?
|
.. _`Sequence Type`:

Sequence Type
Expand Down Expand Up @@ -171,29 +211,33 @@ 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* |
+-----------------------------+-------------------------------------------------------------------+
| -co/\\-\\-codon | Codon codon-based trimming. *Default: off* |
+-----------------------------+-------------------------------------------------------------------+
| -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* |
+-----------------------------+-----------------------------------------------------------------------+


\*Acceptable file formats include:
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51 changes: 46 additions & 5 deletions advanced/index.html
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Expand Up @@ -94,6 +94,8 @@
<li class="toctree-l2"><a class="reference internal" href="#log">Log</a></li>
<li class="toctree-l2"><a class="reference internal" href="#complementary">Complementary</a></li>
<li class="toctree-l2"><a class="reference internal" href="#codon">Codon</a></li>
<li class="toctree-l2"><a class="reference internal" href="#gaps">Gaps</a></li>
<li class="toctree-l2"><a class="reference internal" href="#gap-characters">Gap Characters</a></li>
<li class="toctree-l2"><a class="reference internal" href="#sequence-type">Sequence Type</a></li>
<li class="toctree-l2"><a class="reference internal" href="#all-options">All options</a></li>
</ul>
Expand Down Expand Up @@ -174,6 +176,8 @@ <h1>Advanced Usage<a class="headerlink" href="#advanced-usage" title="Permalink
<li><p><a class="reference internal" href="#log">Log</a></p></li>
<li><p><a class="reference internal" href="#complementary">Complementary</a></p></li>
<li><p><a class="reference internal" href="#codon">Codon</a></p></li>
<li><p><a class="reference internal" href="#gaps">Gaps</a></p></li>
<li><p><a class="reference internal" href="#gap-characters">Gap Characters</a></p></li>
<li><p><a class="reference internal" href="#sequence-type">Sequence Type</a></p></li>
<li><p><a class="reference internal" href="#all-options">All options</a></p></li>
</ul>
Expand Down Expand Up @@ -289,8 +293,39 @@ <h2>Output<a class="headerlink" href="#id2" title="Permalink to this headline">
<div class="line"><br /></div>
</div>
</div>
<div class="section" id="gaps">
<span id="id6"></span><h2>Gaps<a class="headerlink" href="#gaps" title="Permalink to this headline"></a></h2>
<p>Positions with gappyness greater than threshold will be trimmed.
Must be between 0 and 1. (Default: 0.9). This argument is ignored
when using the kpi and kpic mdoes of trimming as well as an
iteration of trimming that uses smart-gap.</p>
<p>To specify a gaps threshold, use the -g/--gaps argument.</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span> clipkit &lt;input&gt; --gaps <span class="m">0</span>.4

<span class="c1"># or</span>

clipkit &lt;input&gt; --g <span class="m">0</span>.4
</pre></div>
</div>
<div class="line-block">
<div class="line"><br /></div>
</div>
</div>
<div class="section" id="gap-characters">
<span id="id7"></span><h2>Gap Characters<a class="headerlink" href="#gap-characters" title="Permalink to this headline"></a></h2>
<p>Specifies gap characters used in the input file. For example,
“NnXx-?” would specify that “N”, “n”, “X”, “x”, “-“, and “?” are
gap characters. Note, the first gap character cannot be “-” because
the parser will interpret the gaps list as a new argument.</p>
<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>clipkit &lt;input&gt; -gc NnXx-?
</pre></div>
</div>
<div class="line-block">
<div class="line"><br /></div>
</div>
</div>
<div class="section" id="sequence-type">
<span id="id6"></span><h2>Sequence Type<a class="headerlink" href="#sequence-type" title="Permalink to this headline"></a></h2>
<span id="id8"></span><h2>Sequence Type<a class="headerlink" href="#sequence-type" title="Permalink to this headline"></a></h2>
<p>Specifies the type of sequences in the input file. The default
is auto-detection of sequence type. Valid options
include aa or nt for amino acids and nucleotides. This argument
Expand All @@ -311,11 +346,11 @@ <h2>Output<a class="headerlink" href="#id2" title="Permalink to this headline">
</div>
</div>
<div class="section" id="all-options">
<span id="id7"></span><h2>All options<a class="headerlink" href="#all-options" title="Permalink to this headline"></a></h2>
<span id="id9"></span><h2>All options<a class="headerlink" href="#all-options" title="Permalink to this headline"></a></h2>
<table class="docutils align-default">
<colgroup>
<col style="width: 30%" />
<col style="width: 70%" />
<col style="width: 29%" />
<col style="width: 71%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
Expand All @@ -338,9 +373,15 @@ <h2>Output<a class="headerlink" href="#id2" title="Permalink to this headline">
<tr class="row-even"><td><p>-g/--gaps</p></td>
<td><p>Specify gappyness threshold (between 0 and 1). <em>Default: 0.9</em></p></td>
</tr>
<tr class="row-odd"><td><p>-co/--codon</p></td>
<tr class="row-odd"><td><p>-gc/--gap_characters</p></td>
<td><p>Specifies gap characters used in input file (AAs: Xx-?*; NTs: XxNn-?*</p></td>
</tr>
<tr class="row-even"><td><p>-co/--codon</p></td>
<td><p>Codon codon-based trimming. <em>Default: off</em></p></td>
</tr>
<tr class="row-odd"><td><p>-s/--sequence</p></td>
<td><p>Specifies sequence type of input file. <em>Default: auto-detect</em></p></td>
</tr>
<tr class="row-even"><td><p>-if/--input_file_format</p></td>
<td><p>Specify input file format*. <em>Default: auto-detect</em></p></td>
</tr>
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2 changes: 2 additions & 0 deletions index.html
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Expand Up @@ -253,6 +253,8 @@ <h1>Quick Start<a class="headerlink" href="#quick-start" title="Permalink to thi
<li class="toctree-l2"><a class="reference internal" href="advanced/index.html#log">Log</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced/index.html#complementary">Complementary</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced/index.html#codon">Codon</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced/index.html#gaps">Gaps</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced/index.html#gap-characters">Gap Characters</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced/index.html#sequence-type">Sequence Type</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced/index.html#all-options">All options</a></li>
</ul>
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