Fix cleavage profile

.github/workflows/static.yml

@@ -0,0 +1,43 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["documentation-update","main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          # Html build
+          path: './docs/_build/html/'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

CHANGELOG.md

@@ -5,6 +5,20 @@ 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).
 
+## [UNRELEASED VERSION]
+
+### Fixed
+- Fixed intersect policy for cleavage_profile
+- Clean up some comments
+- Fixed logging from coverage function
+
+### Added
+- Added numerous util functions
+- Added `left` and `right` options to `cleavage_profile` and CLI
+`cleavage-profile`.
+- Added tests for cleavage profiling.
+
+
 ## [0.5.2] - 2024-05-08
 
 ### Fixed

README.md

@@ -1,90 +1,69 @@
-# FinaleToolkit
-A package and standalone program to extract fragmentation patterns of cell-free
-DNA from paired-end sequencing data. FinaleToolkit refers to FragmentatIoN
-AnaLysis of cEll-free DNA Tools.
-
-FinaleToolkit is in active development, and all API is subject to change and
-should be considered unstable.
+# <img alt="dna with letters FT" src="https://bananasrlowkeygood.github.io/images/finaletools_logo_rounded.png" height="60"> ‎ ‎ ‎FinaleToolkit
+<summary><h3>Table of Contents</h2></summary>
+<ol>
+  <li><a href="#about-the-project">About The Project</a></li>
+  <li><a href="#installation">Installation</a></li>
+  <li>
+    <a href="#usage">Usage</a>
+    <ul>
+      <li><a href="#functionality">Functionality</a></li>
+      <li><a href="#documentation">Documentation</a></li>
+      <li><a href="#compatible-file-formats">Compatible File Formats</a></li>
+      <li><a href="#using-fragment-files">Using Fragment Files</a></li>
+    </ul>
+  </li>
+  <li><a href="#contact">Contact</a></li>
+  <li><a href="#license">License</a></li>
+</ol>
+
+
+
+
+## About The Project
+FinaleToolkit (**F**ragmentat**I**o**N** **A**na**L**ysis of c**E**ll-free DNA **Toolkit**) is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
 
 ## Installation
-Instructions:
-- (Optional) create a conda or venv environment to use FinaleToolkit in.
-- Run `pip install finaletoolkit`
-
-To verify FinaleToolkit has been successfully installed, try
+You can install the package using `pip`.
 ```
-$ 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}
-                   ...
-
-Calculates fragmentation features given a CRAM/BAM/SAM file
-
-options:
-  -h, --help            show this help message and exit
-
-subcommands:
-  {coverage,frag-length,frag-length-bins,frag-length-intervals,wps,delfi,filter-bam,adjust-wps,agg-wps,delfi-gc-correct,end-motifs,mds}
+$ pip install finaletoolkit
 ```
 
 ## Usage
-Documentation can be found at https://epifluidlab.github.io/finaletoolkit-docs/
 
-FinaleToolkit functions generally accept reads in a few file formats:
-- Binary Alignment Map (BAM) Files
-- Compressed Reference-oriented Alignment Map
-- FinaleDB Frag.gz Files
+### Functionality
 
-Frag.gz files are block-gzipped BED3+2 files with the following format:
-`chrom  start  stop  mapq  strand(+/-)`
+FinaleToolkit has support for the following cell-free DNA fragmentation features:
 
-The below script can be used to convert from bam to frag.gz:
-```
-INPUT=input.bam
-OUTPUT=output.frag.gz
-
-samtools sort -n -o qsorted.bam -@ 16 input.bam;
-samtools view -h -f 3 -F 3852 -G 48 --incl-flags 48 \
-  qsorted.bam |\
-  bamToBed -bedpe -mate1 -i stdin |\
-  awk -F'\t' -v OFS="\t" '{if ($1!=$4) next; if ($9=="+") {s=$2;e=$6} else {s=$5;e=$3} if (e>s) print $1,s,e,$8,$9}' |\
-  sort -k1,1V -k2,2n |\
-  bgzip > $OUTPUT;
-tabix -p bed $OUTPUT;
-```
+- Fragment Length
+- Coverage
+- End Motifs
+- Motif Diversity Score [![DOI](https://img.shields.io/badge/DOI-10.1158%2F2159--8290.CD--19--0622-blue?style=flat-square)](https://doi.org/10.1158/2159-8290.CD-19-0622)
+- Windowed Protection Score [![DOI](https://img.shields.io/badge/DOI-110.1016%2Fj.cell.2015.11.050-blue?style=flat-square)](https://doi.org/10.1016/j.cell.2015.11.050)
+- DELFI [![DOI](https://img.shields.io/badge/DOI-10.1038%2Fs41586--019--1272--6-blue?style=flat-square&link=https%3A%2F%2Fdoi.org%2F10.1038%252Fs41586-019-1272-6)](https://doi.org/10.1038%2Fs41586-019-1272-6)
+- Cleavage Profile [![DOI](https://img.shields.io/badge/DOI-10.1073%2Fpnas.2209852119-blue?style=flat-square)](https://doi.org/10.1073/pnas.2209852119)
 
-Frag.gz files can be retrieved from http://finaledb.research.cchmc.org/
+### Documentation
+Documentation for FinaleToolkit can be found [here](https://epifluidlab.github.io/finaletoolkit-docs/).
 
-Because FinaleToolkit uses pysam, BAM files should be bai-indexed and Frag.gz files should be tabix-indexed.
+### Compatible File Formats
 
-To view fragment length distribution
-```
-$ finaletoolkit frag-length-bins --contig 22 --histogram sample.bam
-Fragment Lengths for 22:-
-10.61%                            ▇                              mean      :169.28
-09.85%                           ▆█▁                             median    :169.00
-09.09%                           ███                             stdev     :25.52
-08.34%                           ████                            min       :67.00
-07.58%                          ▁████                            max       :289.00
-06.82%                          █████▂                          
-06.06%                          ██████                          
-05.31%                         ▆██████▂                         
-04.55%                        ▄████████▁                        
-03.79%                       ▃██████████                        
-03.03%                     ▂████████████▆                       
-02.27%                     ██████████████▇▃                     
-01.52%                   ▇█████████████████▅▂                   
-00.76%     ▂▂▂▂▂▂▃▃▄▅▄████████████████████████▆▅▄▃▂▂▂▂▂▂▂▁▁▂▂▂▁▁
-len (nt)067   091   115   139   163   187   211   235   259   283
-```
+FinaleToolkit is compatible with almost any paired-end sequence data:
+
+- Binary Alignment Map (`.bam`) files with an associated index file (`.bam.bai`).
+- Sequence Alignment Map (`.sam`) files.
+- Compressed Reference-oriented Alignment Map (`.cram`) files.
+- Fragment (`.frag.gz`) files with an associated tabix index file (`.frag.gz.tbi`).
+
+### Using Fragment Files
 
-## Testing
+Fragment (`.frag.gz`) files are block-gzipped BED3+2 files with the following columns: `chrom` , `start` , `stop` , `mapq` , `strand`.
 
-To run unit tests, navigate to the root directory of your local copy of this
-repo and run `pytest`. You may have to download pytest first.
+We encourage you to use our comprehensive database, FinaleDB, to access relevant fragment files. Learn more about FinaleDB [here](http://finaledb.research.cchmc.org).
 
-## FAQ
-Q: When running on an ARM64 Mac, I can install FinaleToolkit without errors.
-However, I get an `ImportError` when I run it.
+## Contact
+- James Li: lijw21@wfu.edu
+- Ravi Bandaru: ravi.bandaru@northwestern.edu
+- Yaping Liu: yaping@northwestern.edu
 
-A: Try `brew install curl`. Otherwise, email me and I will try to help you.
+## License
+For academic research, please refer to MIT license. For commerical usage, please contact the authors.

docs/Makefile

@@ -5,8 +5,8 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
+SOURCEDIR     = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/build/html/.buildinfo → docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 6041be4c3e87185b8cc4c04670f254ba
+config: 7b9a79626a3bd201c50461a4a33a6bd0
 tags: 645f666f9bcd5a90fca523b33c5a78b7