From 4197afdb64f2fb5be73234b7c3ab1925eceecec5 Mon Sep 17 00:00:00 2001
From: lucl13 <lucl13@163.com>
Date: Sun, 4 Aug 2024 18:45:51 -0400
Subject: [PATCH] updated docs

---
 docs/build/doctrees/environment.pickle  | Bin 644875 -> 643400 bytes
 docs/build/doctrees/pigeon.doctree      | Bin 19111 -> 17990 bytes
 docs/build/html/_sources/pigeon.rst.txt |  10 ++++------
 docs/build/html/pigeon.html             |  10 ++++------
 docs/build/html/searchindex.js          |   2 +-
 docs/source/pigeon.rst                  |  10 ++++------
 6 files changed, 13 insertions(+), 19 deletions(-)

diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
index d261d2cd7e62fb220c111212eb589aa5bbad4a8e..40b9ba16fd48a56eb048dfa1b87956d564e7ff02 100644
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diff --git a/docs/build/doctrees/pigeon.doctree b/docs/build/doctrees/pigeon.doctree
index 855d3b218bad180aef4377a09de1bfb8a71870b9..a0855cf28024ac4f8d93b2b08a117c465f192332 100644
GIT binary patch
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diff --git a/docs/build/html/_sources/pigeon.rst.txt b/docs/build/html/_sources/pigeon.rst.txt
index ea03987..cd6892e 100644
--- a/docs/build/html/_sources/pigeon.rst.txt
+++ b/docs/build/html/_sources/pigeon.rst.txt
@@ -2,7 +2,7 @@
 PIGEON
 ======
 
-**PIGEON** (Peptide ID Generation for Exchange Of Nuclei) is a stand-only program that takes in a list of peptide pool csv 
+**pigeon** is a stand-only program that takes in a list of peptide pool csv 
 and outputs a cleaned csv of pooled data. It also outputs a rangeslist table for merge in FEATHER.
 
 CMD Options
@@ -11,8 +11,7 @@ CMD Options
 Type ``pigeon --help`` to see the following options:
 
 | ``--t``, ``--table``: Path(s) to input csv. Required
-| ``--b``, ``--batch``:
-| ``--o``, ``--out``: path to output csv. Default: 'CLEAN.csv'
+| ``--o``, ``--out``: path to output csv, if any.
 | ``--p``, ``--plots``: directory for output plots. Default: './csvplots'
 | ``--ov``, ``--overlap``: flag specifying how to treat overlapping duplicates. Options: 'keep', 'drop', 'select' (or any other). Default: 'select'
 | ``--r``, ``--rangeslist``: path to output rangeslist, if any.
@@ -25,11 +24,10 @@ Type ``pigeon --help`` to see the following options:
 Default inputs
 
 | ``--t`` (list of peptide pool csvs)
-| ``--b`` (table for batched data. Each row contains 'name' string for protein, then all pool csvs corresponding to that pool)
 
 Default outputs
   
-| ``--o`` (batched and cleaned peptide pool csv): ``CLEAN.csv``
+| ``--o`` (batched and cleaned peptide pool csv)
 | ``--r`` (rangeslist table for merge in post-PIGEON)
 
 In the plot directory, the following files are generated:
@@ -72,4 +70,4 @@ Alternative usage example:
 
 .. code-block:: bash
 
-   pigeon biotools-cleaner.py --b batch-list.txt --p csvplots --ov select --o select-pooled.csv
+   pigeon --t pool-1.csv --o select-pooled.csv --r rangeslist.csv
diff --git a/docs/build/html/pigeon.html b/docs/build/html/pigeon.html
index 10195e3..a8fede7 100644
--- a/docs/build/html/pigeon.html
+++ b/docs/build/html/pigeon.html
@@ -90,15 +90,14 @@
              
   <section id="pigeon">
 <h1>PIGEON<a class="headerlink" href="#pigeon" title="Link to this heading"></a></h1>
-<p><strong>PIGEON</strong> (Peptide ID Generation for Exchange Of Nuclei) is a stand-only program that takes in a list of peptide pool csv
+<p><strong>pigeon</strong> is a stand-only program that takes in a list of peptide pool csv
 and outputs a cleaned csv of pooled data. It also outputs a rangeslist table for merge in FEATHER.</p>
 <section id="cmd-options">
 <h2>CMD Options<a class="headerlink" href="#cmd-options" title="Link to this heading"></a></h2>
 <p>Type <code class="docutils literal notranslate"><span class="pre">pigeon</span> <span class="pre">--help</span></code> to see the following options:</p>
 <div class="line-block">
 <div class="line"><code class="docutils literal notranslate"><span class="pre">--t</span></code>, <code class="docutils literal notranslate"><span class="pre">--table</span></code>: Path(s) to input csv. Required</div>
-<div class="line"><code class="docutils literal notranslate"><span class="pre">--b</span></code>, <code class="docutils literal notranslate"><span class="pre">--batch</span></code>:</div>
-<div class="line"><code class="docutils literal notranslate"><span class="pre">--o</span></code>, <code class="docutils literal notranslate"><span class="pre">--out</span></code>: path to output csv. Default: ‘CLEAN.csv’</div>
+<div class="line"><code class="docutils literal notranslate"><span class="pre">--o</span></code>, <code class="docutils literal notranslate"><span class="pre">--out</span></code>: path to output csv, if any.</div>
 <div class="line"><code class="docutils literal notranslate"><span class="pre">--p</span></code>, <code class="docutils literal notranslate"><span class="pre">--plots</span></code>: directory for output plots. Default: ‘./csvplots’</div>
 <div class="line"><code class="docutils literal notranslate"><span class="pre">--ov</span></code>, <code class="docutils literal notranslate"><span class="pre">--overlap</span></code>: flag specifying how to treat overlapping duplicates. Options: ‘keep’, ‘drop’, ‘select’ (or any other). Default: ‘select’</div>
 <div class="line"><code class="docutils literal notranslate"><span class="pre">--r</span></code>, <code class="docutils literal notranslate"><span class="pre">--rangeslist</span></code>: path to output rangeslist, if any.</div>
@@ -111,11 +110,10 @@ <h2>CMD Options<a class="headerlink" href="#cmd-options" title="Link to this hea
 <p>Default inputs</p>
 <div class="line-block">
 <div class="line"><code class="docutils literal notranslate"><span class="pre">--t</span></code> (list of peptide pool csvs)</div>
-<div class="line"><code class="docutils literal notranslate"><span class="pre">--b</span></code> (table for batched data. Each row contains ‘name’ string for protein, then all pool csvs corresponding to that pool)</div>
 </div>
 <p>Default outputs</p>
 <div class="line-block">
-<div class="line"><code class="docutils literal notranslate"><span class="pre">--o</span></code> (batched and cleaned peptide pool csv): <code class="docutils literal notranslate"><span class="pre">CLEAN.csv</span></code></div>
+<div class="line"><code class="docutils literal notranslate"><span class="pre">--o</span></code> (batched and cleaned peptide pool csv)</div>
 <div class="line"><code class="docutils literal notranslate"><span class="pre">--r</span></code> (rangeslist table for merge in post-PIGEON)</div>
 </div>
 <p>In the plot directory, the following files are generated:</p>
@@ -155,7 +153,7 @@ <h2>Example Usage<a class="headerlink" href="#example-usage" title="Link to this
 </pre></div>
 </div>
 <p>Alternative usage example:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pigeon<span class="w"> </span>biotools-cleaner.py<span class="w"> </span>--b<span class="w"> </span>batch-list.txt<span class="w"> </span>--p<span class="w"> </span>csvplots<span class="w"> </span>--ov<span class="w"> </span><span class="k">select</span><span class="w"> </span>--o<span class="w"> </span><span class="k">select</span>-pooled.csv
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pigeon<span class="w"> </span>--t<span class="w"> </span>pool-1.csv<span class="w"> </span>--o<span class="w"> </span><span class="k">select</span>-pooled.csv<span class="w"> </span>--r<span class="w"> </span>rangeslist.csv
 </pre></div>
 </div>
 </section>
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 1174b9c..6ea59a2 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
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\ No newline at end of file
diff --git a/docs/source/pigeon.rst b/docs/source/pigeon.rst
index ea03987..cd6892e 100644
--- a/docs/source/pigeon.rst
+++ b/docs/source/pigeon.rst
@@ -2,7 +2,7 @@
 PIGEON
 ======
 
-**PIGEON** (Peptide ID Generation for Exchange Of Nuclei) is a stand-only program that takes in a list of peptide pool csv 
+**pigeon** is a stand-only program that takes in a list of peptide pool csv 
 and outputs a cleaned csv of pooled data. It also outputs a rangeslist table for merge in FEATHER.
 
 CMD Options
@@ -11,8 +11,7 @@ CMD Options
 Type ``pigeon --help`` to see the following options:
 
 | ``--t``, ``--table``: Path(s) to input csv. Required
-| ``--b``, ``--batch``:
-| ``--o``, ``--out``: path to output csv. Default: 'CLEAN.csv'
+| ``--o``, ``--out``: path to output csv, if any.
 | ``--p``, ``--plots``: directory for output plots. Default: './csvplots'
 | ``--ov``, ``--overlap``: flag specifying how to treat overlapping duplicates. Options: 'keep', 'drop', 'select' (or any other). Default: 'select'
 | ``--r``, ``--rangeslist``: path to output rangeslist, if any.
@@ -25,11 +24,10 @@ Type ``pigeon --help`` to see the following options:
 Default inputs
 
 | ``--t`` (list of peptide pool csvs)
-| ``--b`` (table for batched data. Each row contains 'name' string for protein, then all pool csvs corresponding to that pool)
 
 Default outputs
   
-| ``--o`` (batched and cleaned peptide pool csv): ``CLEAN.csv``
+| ``--o`` (batched and cleaned peptide pool csv)
 | ``--r`` (rangeslist table for merge in post-PIGEON)
 
 In the plot directory, the following files are generated:
@@ -72,4 +70,4 @@ Alternative usage example:
 
 .. code-block:: bash
 
-   pigeon biotools-cleaner.py --b batch-list.txt --p csvplots --ov select --o select-pooled.csv
+   pigeon --t pool-1.csv --o select-pooled.csv --r rangeslist.csv