epifluidlab · jamesli124 · Apr 30, 2024 · Apr 5, 2024 · Apr 9, 2024 · Apr 24, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,24 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.5.0] - 2024-04-24
+
+### Added
+- Added finaletools.interval_end_motifs function to calculate end-motifs
+over genomic intervals. Stores results in an IntervalEndMotifs object.
+- Added CLI subcommand interval-end-motifs to calculate end-motifs over
+genomic intervals.
+- Added CLI subcommand interval-mds to calculate MDS over intervals from
+interval end-motifs table.
+
+### Changed
+- Added gc_correct option to delfi_merge_bins so that merging is possible
+without GC correction
+
+### Fixed
+- `delfi` can now be run with `gc_correct=false` and `merge_bins=true`
+- fixed `cleavage_profile` import in `frag`
+
 ## [0.4.5] - 2024-04-9
 
 ### Added

diff --git a/README.md b/README.md
@@ -1,20 +1,20 @@
-# FinaleTools
+# FinaleToolkit
 A package and standalone program to extract fragmentation patterns of cell-free
-DNA from paired-end sequencing data. FinaleTools refers to FragmentatIoN
+DNA from paired-end sequencing data. FinaleToolkit refers to FragmentatIoN
 AnaLysis of cEll-free DNA Tools.
 
-FinaleTools is in active development, and all API is subject to change and
+FinaleToolkit is in active development, and all API is subject to change and
 should be considered unstable.
 
 ## Installation
 Instructions:
-- (Optional) create a conda or venv environment to use FinaleTools in.
-- Run `pip install finaletools`
+- (Optional) create a conda or venv environment to use FinaleToolkit in.
+- Run `pip install finaletoolkit`
 
-To verify FinaleTools has been successfully installed, try
+To verify FinaleToolkit has been successfully installed, try
 ```
-$ finaletools -h
-usage: finaletools [-h]
+$ finaletoolkit -h
+usage: finaletoolkit [-h]
                    {coverage,frag-length,frag-length-bins,frag-length-intervals,wps,delfi,filter-bam,adjust-wps,agg-wps,delfi-gc-correct,end-motifs,mds}
                    ...
 
@@ -28,9 +28,9 @@ subcommands:
 ```
 
 ## Usage
-Documentation can be found at https://epifluidlab.github.io/finaletools-docs/
+Documentation can be found at https://epifluidlab.github.io/finaletoolkit-docs/
 
-FinaleTools functions generally accept reads in a few file formats:
+FinaleToolkit functions generally accept reads in a few file formats:
 - Binary Alignment Map (BAM) Files
 - Compressed Reference-oriented Alignment Map
 - FinaleDB Frag.gz Files
@@ -55,11 +55,11 @@ tabix -p bed $OUTPUT;
 
 Frag.gz files can be retrieved from http://finaledb.research.cchmc.org/
 
-Because FinaleTools uses pysam, BAM files should be bai-indexed and Frag.gz files should be tabix-indexed.
+Because FinaleToolkit uses pysam, BAM files should be bai-indexed and Frag.gz files should be tabix-indexed.
 
 To view fragment length distribution
 ```
-$ finaletools frag-length-bins --contig 22 --histogram sample.bam
+$ finaletoolkit frag-length-bins --contig 22 --histogram sample.bam
 Fragment Lengths for 22:-
 10.61%                            ▇                              mean      :169.28
 09.85%                           ▆█▁                             median    :169.00
@@ -79,7 +79,7 @@ len (nt)067   091   115   139   163   187   211   235   259   283
 ```
 
 ## FAQ
-Q: When running on an ARM64 Mac, I can install FinaleTools without errors.
+Q: When running on an ARM64 Mac, I can install FinaleToolkit without errors.
 However, I get an `ImportError` when I run it.
 
 A: Try `brew install curl`. Otherwise, email me and I will try to help you.
diff --git a/docs/build/doctrees/api.doctree b/docs/build/doctrees/api.doctree
diff --git a/docs/build/doctrees/cli.doctree b/docs/build/doctrees/cli.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/quick_start.doctree b/docs/build/doctrees/quick_start.doctree
diff --git a/docs/build/doctrees/releases.doctree b/docs/build/doctrees/releases.doctree
diff --git a/docs/build/doctrees/usage.doctree b/docs/build/doctrees/usage.doctree
diff --git a/docs/build/html/_sources/api.rst.txt b/docs/build/html/_sources/api.rst.txt
@@ -29,16 +29,28 @@ DELFI
 
 .. autofunction:: finaletools.frag.delfi_gc_correct
 
+.. autofunction:: finaletools.frag.delfi_merge_bins
+
 End-motifs
 ==========
 
 .. autoclass:: finaletools.frag.EndMotifFreqs
    :members:
 
+.. autoclass:: finaletools.frag.EndMotifsIntervals
+   :members:
+
 .. autofunction:: finaletools.frag.region_end_motifs
 
 .. autofunction:: finaletools.frag.end_motifs
 
+.. autofunction:: finaletools.frag.interval_end_motifs
+
+Cleavage Profile
+================
+.. autofunction:: finaletools.frag.cleavage_profile
+
+
 Frag File Utilities
 ===================
 

diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
@@ -15,7 +15,6 @@ Welcome to FinaleTools's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-   usage
    quick_start
    cli
    api

diff --git a/docs/build/html/api.html b/docs/build/html/api.html
diff --git a/docs/build/html/cli.html b/docs/build/html/cli.html
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
@@ -117,10 +117,12 @@ <h2 id="B">B</h2>
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api.html#finaletools.genome.ContigGaps">ContigGaps (class in finaletools.genome)</a>
+      <li><a href="api.html#finaletools.frag.cleavage_profile">cleavage_profile() (in module finaletools.frag)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api.html#finaletools.genome.ContigGaps">ContigGaps (class in finaletools.genome)</a>
+</li>
       <li><a href="api.html#finaletools.frag.coverage">coverage() (in module finaletools.frag)</a>
 </li>
   </ul></td>
@@ -134,6 +136,8 @@ <h2 id="D">D</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api.html#finaletools.frag.delfi_gc_correct">delfi_gc_correct() (in module finaletools.frag)</a>
+</li>
+      <li><a href="api.html#finaletools.frag.delfi_merge_bins">delfi_merge_bins() (in module finaletools.frag)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -146,6 +150,8 @@ <h2 id="E">E</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api.html#finaletools.frag.EndMotifFreqs">EndMotifFreqs (class in finaletools.frag)</a>
+</li>
+      <li><a href="api.html#finaletools.frag.EndMotifsIntervals">EndMotifsIntervals (class in finaletools.frag)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -156,13 +162,19 @@ <h2 id="F">F</h2>
       <li><a href="api.html#finaletools.utils.filter_bam">filter_bam() (in module finaletools.utils)</a>
 </li>
       <li><a href="api.html#finaletools.frag.frag_length">frag_length() (in module finaletools.frag)</a>
+</li>
+      <li><a href="api.html#finaletools.frag.frag_length_bins">frag_length_bins() (in module finaletools.frag)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api.html#finaletools.frag.frag_length_bins">frag_length_bins() (in module finaletools.frag)</a>
+      <li><a href="api.html#finaletools.frag.EndMotifsIntervals.freq">freq() (finaletools.frag.EndMotifsIntervals method)</a>
 </li>
       <li><a href="api.html#finaletools.frag.EndMotifFreqs.from_file">from_file() (finaletools.frag.EndMotifFreqs class method)</a>
+
+      <ul>
+        <li><a href="api.html#finaletools.frag.EndMotifsIntervals.from_file">(finaletools.frag.EndMotifsIntervals class method)</a>
 </li>
+      </ul></li>
   </ul></td>
 </tr></table>
 
@@ -191,22 +203,30 @@ <h2 id="I">I</h2>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api.html#finaletools.genome.ContigGaps.in_gap">in_gap() (finaletools.genome.ContigGaps method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api.html#finaletools.genome.ContigGaps.in_tcmere">in_tcmere() (finaletools.genome.ContigGaps method)</a>
 
       <ul>
         <li><a href="api.html#finaletools.genome.GenomeGaps.in_tcmere">(finaletools.genome.GenomeGaps method)</a>
 </li>
       </ul></li>
   </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api.html#finaletools.frag.interval_end_motifs">interval_end_motifs() (in module finaletools.frag)</a>
+</li>
+  </ul></td>
 </tr></table>
 
 <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api.html#finaletools.frag.EndMotifsIntervals.mds_bed">mds_bed() (finaletools.frag.EndMotifsIntervals method)</a>
+</li>
       <li><a href="api.html#finaletools.frag.EndMotifFreqs.motif_diversity_score">motif_diversity_score() (finaletools.frag.EndMotifFreqs method)</a>
+
+      <ul>
+        <li><a href="api.html#finaletools.frag.EndMotifsIntervals.motif_diversity_score">(finaletools.frag.EndMotifsIntervals method)</a>
 </li>
+      </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="api.html#finaletools.frag.multi_wps">multi_wps() (in module finaletools.frag)</a>
@@ -233,12 +253,22 @@ <h2 id="R">R</h2>
 <h2 id="T">T</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="api.html#finaletools.genome.GenomeGaps.to_bed">to_bed() (finaletools.genome.GenomeGaps method)</a>
+      <li><a href="api.html#finaletools.frag.EndMotifsIntervals.to_bed">to_bed() (finaletools.frag.EndMotifsIntervals method)</a>
+
+      <ul>
+        <li><a href="api.html#finaletools.genome.GenomeGaps.to_bed">(finaletools.genome.GenomeGaps method)</a>
 </li>
+      </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="api.html#finaletools.frag.EndMotifsIntervals.to_bedgraph">to_bedgraph() (finaletools.frag.EndMotifsIntervals method)</a>
+</li>
       <li><a href="api.html#finaletools.frag.EndMotifFreqs.to_tsv">to_tsv() (finaletools.frag.EndMotifFreqs method)</a>
+
+      <ul>
+        <li><a href="api.html#finaletools.frag.EndMotifsIntervals.to_tsv">(finaletools.frag.EndMotifsIntervals method)</a>
 </li>
+      </ul></li>
   </ul></td>
 </tr></table>
 

diff --git a/docs/build/html/index.html b/docs/build/html/index.html
@@ -98,6 +98,7 @@ <h1>Welcome to FinaleTools’s documentation!<a class="headerlink" href="#welcom
 <li class="toctree-l2"><a class="reference internal" href="api.html#window-protection-score">Window Protection Score</a></li>
 <li class="toctree-l2"><a class="reference internal" href="api.html#delfi">DELFI</a></li>
 <li class="toctree-l2"><a class="reference internal" href="api.html#end-motifs">End-motifs</a></li>
+<li class="toctree-l2"><a class="reference internal" href="api.html#cleavage-profile">Cleavage Profile</a></li>
 <li class="toctree-l2"><a class="reference internal" href="api.html#frag-file-utilities">Frag File Utilities</a></li>
 <li class="toctree-l2"><a class="reference internal" href="api.html#genome-utilities">Genome Utilities</a></li>
 </ul>

diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
diff --git a/docs/build/html/quick_start.html b/docs/build/html/quick_start.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Quick-start Guide &mdash; FinaleTools  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -20,7 +22,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="CLI" href="cli.html" />
-    <link rel="prev" title="Welcome to FinaleTools’s documentation!" href="index.html" /> 
+    <link rel="prev" title="Usage" href="usage.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -44,6 +46,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Quick-start Guide</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#installation">Installation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#usage">Usage</a></li>
@@ -172,7 +175,7 @@ <h2>Usage<a class="headerlink" href="#usage" title="Permalink to this heading">
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="index.html" class="btn btn-neutral float-left" title="Welcome to FinaleTools’s documentation!" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="usage.html" class="btn btn-neutral float-left" title="Usage" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="cli.html" class="btn btn-neutral float-right" title="CLI" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

diff --git a/docs/build/html/releases.html b/docs/build/html/releases.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Releases &mdash; FinaleTools  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -43,6 +45,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
 <li class="toctree-l1"><a class="reference internal" href="quick_start.html">Quick-start Guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="cli.html">CLI</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api.html">API</a></li>

diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
-Original file line number
+Diff line change
@@ Expand Up / @@ -15,7 +15,6 @@ Welcome to FinaleTools's documentation! @@
        :maxdepth: 2
        :caption: Contents:
-       usage
        quick_start
        cli
        api
@@ Expand Down @@