DAJIN2 0.1.32a0__zip → 0.3.2__zip

{DAJIN2-0.1.32a0 → DAJIN2-0.3.2}/MANIFEST.in

@@ -1,3 +1,6 @@
+include requirements.txt
 include src/DAJIN2/template_igvjs.html
+
 graft src/DAJIN2/templates
 graft src/DAJIN2/static
+graft src/DAJIN2/utils

DAJIN2-0.3.2/PKG-INFO

@@ -0,0 +1,258 @@
+Metadata-Version: 2.1
+Name: DAJIN2
+Version: 0.3.2
+Summary: One-step genotyping tools for targeted long-read sequencing
+Home-page: https://github.com/akikuno/DAJIN2
+Author: Akihiro Kuno
+Author-email: akuno@md.tsukuba.ac.jp
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: MacOS
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+[![License](https://img.shields.io/badge/License-MIT-9cf.svg?style=flat-square)](https://choosealicense.com/licenses/mit/)
+[![Test](https://img.shields.io/github/actions/workflow/status/akikuno/dajin2/pytest.yml?branch=main&label=Test&color=brightgreen&style=flat-square)](https://github.com/akikuno/dajin2/actions)
+[![Python](https://img.shields.io/pypi/pyversions/DAJIN2.svg?label=Python&color=blue&style=flat-square)](https://pypi.org/project/DAJIN2/)
+[![PyPI](https://img.shields.io/pypi/v/DAJIN2.svg?label=PyPI&color=orange&style=flat-square)](https://pypi.org/project/DAJIN2/)
+[![Bioconda](https://img.shields.io/conda/v/bioconda/dajin2?label=Bioconda&color=orange&style=flat-square)](https://anaconda.org/bioconda/dajin2)
+[![DOI](https://zenodo.org/badge/387721337.svg)](https://zenodo.org/badge/latestdoi/387721337)
+
+
+<p align="center">
+<img src="https://user-images.githubusercontent.com/15861316/261833016-7f356960-88cf-4574-87e2-36162b174340.png" width="90%">
+</p>
+
+[日本語はこちら](https://github.com/akikuno/DAJIN2/blob/main/docs/README_JP.md)
+
+DAJIN2 is a genotyping software designed for organisms that have undergone genome editing, utilizing nanopore sequencing technology.  
+
+The name DAJIN is inspired by the term 一網**打尽** (Ichimou **DAJIN** or Yīwǎng **Dǎjìn**), which signifies capturing everything in a single net.  
+
+## 🙏 Feedbacks
+
+DAJIN2 is still in the development phase.  
+Basic tests covering point mutations, deletions, and insertion designs have been conducted.  
+If you encounter any bugs or issues, please report them via [Issues](https://github.com/akikuno/DAJIN2/issues).  
+
+
+
+## 🛠 Installation
+
+### From [Bioconda](https://anaconda.org/bioconda/DAJIN2) (Recommended)
+
+```bash
+conda install -c bioconda DAJIN2
+```
+
+### From [PyPI](https://pypi.org/project/DAJIN2/)
+
+```bash
+pip install DAJIN2
+```
+
+> **Warning**  
+> If you encounter the error **Failed to build mappy** when installing DAJIN2 from pip, please install `gcc` and `zlib`.  
+> `sudo apt install gcc zlib1g zlib1g-dev` (Ubuntu)  
+> `brew install gcc zlib` (macOS)
+
+<!-- ```bash
+# Ubuntu
+sudo apt install gcc zlib1g zlib1g-dev
+```
+
+```bash
+# macOS
+brew install gcc zlib
+``` -->
+
+
+## 💡 Usage
+
+### Single Sample Analysis
+
+DAJIN2 allows for the analysis of single samples (one sample vs one control).
+
+```bash
+DAJIN2 <-s|--sample> <-c|--control> <-a|--allele> <-n|--name> [-g|--genome] [-t|--threads] [-h|--help] [-v|--version]
+
+options:
+  -s, --sample              Path to a sample FASTQ file
+  -c, --control             Path to a control FASTQ file
+  -a, --allele              Path to a FASTA file
+  -n, --name                Output directory name
+  -g, --genome (Optional)   Reference genome ID (e.g hg38, mm39) [default: '']
+  -t, --threads (Optional)  Number of threads [default: 1]
+  -h, --help                show this help message and exit
+  -v, --version             show the version number and exit
+```
+
+#### Example
+
+```bash
+# Donwload the example dataset
+wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-single.tar.gz
+tar -xf example-single.tar.gz
+
+# Run DAJIN2
+DAJIN2 \
+    --name stx2-deletion \
+    --sample example-single/sample.fq.gz \
+    --control example-single/control.fq.gz \
+    --allele example-single/design.fa \
+    --genome mm39 \
+    --threads 10
+
+# 2023-06-04 11:30:03: example-single/control.fq.gz is now processing...
+# 2023-06-04 11:30:06: Preprocess example-single/control.fq.gz...
+# 2023-06-04 11:30:06: Mapping example-single/control.fq.gz...
+# 2023-06-04 11:30:21: Call MIDSV example-single/control.fq.gz...
+# 2023-06-04 11:30:31: 🍵 example-single/control.fq.gz is finished!
+# 2023-06-04 11:30:31: example-single/sample.fq.gz is now processing...
+# 2023-06-04 11:30:35: Preprocess example-single/sample.fq.gz...
+# 2023-06-04 11:34:13: Classify example-single/sample.fq.gz...
+# 2023-06-04 11:34:18: Clustering example-single/sample.fq.gz...
+# 2023-06-04 11:35:01: Consensus calling example-single/sample.fq.gz...
+# 2023-06-04 11:35:08: 🍵 example-single/sample.fq.gz is finished!
+# 🎉 Finished! Open DAJIN_Results/stx2-deletion to see the report.
+```
+
+### Batch Processing
+
+By using the `batch` subcommand, you can process multiple FASTQ files simultaneously.  
+For this purpose, a CSV or Excel file consolidating the sample information is required.  
+For a specific example, please refer to [this link](https://github.com/akikuno/DAJIN2/blob/main/examples/example-batch/batch.csv).
+
+
+```bash
+DAJIN2 batch <-f|--file> [-t|--threads] [-h]
+
+options:
+  -f, --file                Path to a CSV or Excel file
+  -t, --threads (Optional)  Number of threads [default: 1]
+  -h, --help                Show this help message and exit
+```
+
+#### Example
+
+```bash
+# Donwload the example dataset
+wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-batch.tar.gz
+tar -xf example-batch.tar.gz
+
+# Run DAJIN2
+DAJIN2 batch --file example-batch/batch.csv --threads 3
+
+# 2023-07-31 17:01:10: example-batch/tyr_control.fq.gz is now processing...
+# 2023-07-31 17:01:16: Preprocess example-batch/tyr_control.fq.gz...
+# 2023-07-31 17:01:48: Output BAM files of example-batch/tyr_control.fq.gz...
+# 2023-07-31 17:01:52: 🍵 example-batch/tyr_control.fq.gz is finished!
+# 2023-07-31 17:01:52: example-batch/tyr_c230gt_50%.fq.gz is now processing...
+# 2023-07-31 17:01:52: example-batch/tyr_c230gt_10%.fq.gz is now processing...
+# 2023-07-31 17:01:52: example-batch/tyr_c230gt_01%.fq.gz is now processing...
+# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:02:17: Classify example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:02:19: Clustering example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:02:34: Classify example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:02:35: Classify example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:02:39: Clustering example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:02:39: Clustering example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:02:53: Consensus calling of example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:02:59: Output reports of example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:03:04: 🍵 example-batch/tyr_c230gt_50%.fq.gz is finished!
+# 2023-07-31 17:03:39: Consensus calling of example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:03:51: Output reports of example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:04:03: 🍵 example-batch/tyr_c230gt_01%.fq.gz is finished!
+# 2023-07-31 17:04:08: Consensus calling of example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:04:16: Output reports of example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:04:24: 🍵 example-batch/tyr_c230gt_10%.fq.gz is finished!
+# 🎉 Finished! Open DAJIN_Results/tyr-substitution to see the report.
+```
+
+## 📈 Report Contents
+
+Upon completion of DAJIN2 processing, a directory named **DAJIN_Results** is generated.  
+Inside the **DAJIN_Results** directory, the following files can be found:  
+
+```
+DAJIN_Results/tyr-substitution
+├── BAM
+│   ├── tyr_c230gt_01%
+│   ├── tyr_c230gt_10%
+│   ├── tyr_c230gt_50%
+│   └── tyr_control
+├── FASTA
+│   ├── tyr_c230gt_01%
+│   ├── tyr_c230gt_10%
+│   └── tyr_c230gt_50%
+├── HTML
+│   ├── tyr_c230gt_01%
+│   ├── tyr_c230gt_10%
+│   └── tyr_c230gt_50%
+├── MUTATION_INFO
+│   ├── tyr_c230gt_01%.csv
+│   ├── tyr_c230gt_10%.csv
+│   └── tyr_c230gt_50%.csv
+├── read_all.csv
+├── read_plot.html
+├── read_plot.pdf
+└── read_summary.csv
+```
+
+### 1. BAM
+
+The BAM directory contains the BAM files of reads classified per allele.  
+
+> **Note**  
+> Specifying a reference genome using the `genome` option will align the reads to that genome.  
+> Without `genome` options, the reads will align to the control allele within the input FASTA file.
+
+### 2. FASTA and HTML
+
+The FASTA directory stores the FASTA files of each allele.  
+The HTML directory contains HTML files for each allele, where mutation sites are color-highlighted.  
+For example, Tyr point mutation is highlighted in **green**.  
+
+<img src="https://user-images.githubusercontent.com/15861316/274518501-2ca3f442-1b86-4635-be3d-fd37575c4ca2.png" width="75%" />
+
+### 3. MUTATION_INFO
+
+The MUTATION_INFO directory saves tables depicting mutation sites for each allele.  
+An example of a Tyr point mutation is described by its position on the chromosome and the type of mutation.  
+
+<img src="https://user-images.githubusercontent.com/15861316/274519342-a613490d-5dbb-4a27-a2cf-bca0686b30f0.png" width="75%">
+
+### 4. read_plot.html and read_plot.pdf
+
+Both read_plot.html and read_plot.pdf illustrate the proportions of each allele.  
+The chart's **Allele type** indicates the type of allele, and **% of reads** shows the proportion of reads for that allele.  
+
+Additionally, the types of **Allele type** include:
+- **intact**: Alleles that perfectly match the input FASTA allele.
+- **indels**: Substitutions, deletions, insertions, or inversions within 50 bases.
+- **sv**: Substitutions, deletions, insertions, or inversions beyond 50 bases.
+
+<img src="https://user-images.githubusercontent.com/15861316/274521067-4d217251-4c62-4dc9-9c05-7f5377dd3025.png" width="75%">
+
+> **Warning**  
+> In PCR amplicon sequencing, the % of reads might not match the actual allele proportions due to amplification bias.  
+> Especially when large deletions are present, the deletion alleles might be significantly amplified, potentially not reflecting the actual allele proportions.
+
+### 5. read_all.csv and read_summary.csv
+
+- read_all.csv: Records which allele each read is classified under.  
+- read_summary.csv: Describes the number of reads and presence proportion for each allele.  
+
+
+## 📄 References
+
+For more information, please refer to the following publication:
+
+[Kuno A, et al. (2022) DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes. *PLoS Biology* 20(1): e3001507.](https://doi.org/10.1371/journal.pbio.3001507)

DAJIN2-0.3.2/README.md

@@ -0,0 +1,240 @@
+[![License](https://img.shields.io/badge/License-MIT-9cf.svg?style=flat-square)](https://choosealicense.com/licenses/mit/)
+[![Test](https://img.shields.io/github/actions/workflow/status/akikuno/dajin2/pytest.yml?branch=main&label=Test&color=brightgreen&style=flat-square)](https://github.com/akikuno/dajin2/actions)
+[![Python](https://img.shields.io/pypi/pyversions/DAJIN2.svg?label=Python&color=blue&style=flat-square)](https://pypi.org/project/DAJIN2/)
+[![PyPI](https://img.shields.io/pypi/v/DAJIN2.svg?label=PyPI&color=orange&style=flat-square)](https://pypi.org/project/DAJIN2/)
+[![Bioconda](https://img.shields.io/conda/v/bioconda/dajin2?label=Bioconda&color=orange&style=flat-square)](https://anaconda.org/bioconda/dajin2)
+[![DOI](https://zenodo.org/badge/387721337.svg)](https://zenodo.org/badge/latestdoi/387721337)
+
+
+<p align="center">
+<img src="https://user-images.githubusercontent.com/15861316/261833016-7f356960-88cf-4574-87e2-36162b174340.png" width="90%">
+</p>
+
+[日本語はこちら](https://github.com/akikuno/DAJIN2/blob/main/docs/README_JP.md)
+
+DAJIN2 is a genotyping software designed for organisms that have undergone genome editing, utilizing nanopore sequencing technology.  
+
+The name DAJIN is inspired by the term 一網**打尽** (Ichimou **DAJIN** or Yīwǎng **Dǎjìn**), which signifies capturing everything in a single net.  
+
+## 🙏 Feedbacks
+
+DAJIN2 is still in the development phase.  
+Basic tests covering point mutations, deletions, and insertion designs have been conducted.  
+If you encounter any bugs or issues, please report them via [Issues](https://github.com/akikuno/DAJIN2/issues).  
+
+
+
+## 🛠 Installation
+
+### From [Bioconda](https://anaconda.org/bioconda/DAJIN2) (Recommended)
+
+```bash
+conda install -c bioconda DAJIN2
+```
+
+### From [PyPI](https://pypi.org/project/DAJIN2/)
+
+```bash
+pip install DAJIN2
+```
+
+> **Warning**  
+> If you encounter the error **Failed to build mappy** when installing DAJIN2 from pip, please install `gcc` and `zlib`.  
+> `sudo apt install gcc zlib1g zlib1g-dev` (Ubuntu)  
+> `brew install gcc zlib` (macOS)
+
+<!-- ```bash
+# Ubuntu
+sudo apt install gcc zlib1g zlib1g-dev
+```
+
+```bash
+# macOS
+brew install gcc zlib
+``` -->
+
+
+## 💡 Usage
+
+### Single Sample Analysis
+
+DAJIN2 allows for the analysis of single samples (one sample vs one control).
+
+```bash
+DAJIN2 <-s|--sample> <-c|--control> <-a|--allele> <-n|--name> [-g|--genome] [-t|--threads] [-h|--help] [-v|--version]
+
+options:
+  -s, --sample              Path to a sample FASTQ file
+  -c, --control             Path to a control FASTQ file
+  -a, --allele              Path to a FASTA file
+  -n, --name                Output directory name
+  -g, --genome (Optional)   Reference genome ID (e.g hg38, mm39) [default: '']
+  -t, --threads (Optional)  Number of threads [default: 1]
+  -h, --help                show this help message and exit
+  -v, --version             show the version number and exit
+```
+
+#### Example
+
+```bash
+# Donwload the example dataset
+wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-single.tar.gz
+tar -xf example-single.tar.gz
+
+# Run DAJIN2
+DAJIN2 \
+    --name stx2-deletion \
+    --sample example-single/sample.fq.gz \
+    --control example-single/control.fq.gz \
+    --allele example-single/design.fa \
+    --genome mm39 \
+    --threads 10
+
+# 2023-06-04 11:30:03: example-single/control.fq.gz is now processing...
+# 2023-06-04 11:30:06: Preprocess example-single/control.fq.gz...
+# 2023-06-04 11:30:06: Mapping example-single/control.fq.gz...
+# 2023-06-04 11:30:21: Call MIDSV example-single/control.fq.gz...
+# 2023-06-04 11:30:31: 🍵 example-single/control.fq.gz is finished!
+# 2023-06-04 11:30:31: example-single/sample.fq.gz is now processing...
+# 2023-06-04 11:30:35: Preprocess example-single/sample.fq.gz...
+# 2023-06-04 11:34:13: Classify example-single/sample.fq.gz...
+# 2023-06-04 11:34:18: Clustering example-single/sample.fq.gz...
+# 2023-06-04 11:35:01: Consensus calling example-single/sample.fq.gz...
+# 2023-06-04 11:35:08: 🍵 example-single/sample.fq.gz is finished!
+# 🎉 Finished! Open DAJIN_Results/stx2-deletion to see the report.
+```
+
+### Batch Processing
+
+By using the `batch` subcommand, you can process multiple FASTQ files simultaneously.  
+For this purpose, a CSV or Excel file consolidating the sample information is required.  
+For a specific example, please refer to [this link](https://github.com/akikuno/DAJIN2/blob/main/examples/example-batch/batch.csv).
+
+
+```bash
+DAJIN2 batch <-f|--file> [-t|--threads] [-h]
+
+options:
+  -f, --file                Path to a CSV or Excel file
+  -t, --threads (Optional)  Number of threads [default: 1]
+  -h, --help                Show this help message and exit
+```
+
+#### Example
+
+```bash
+# Donwload the example dataset
+wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-batch.tar.gz
+tar -xf example-batch.tar.gz
+
+# Run DAJIN2
+DAJIN2 batch --file example-batch/batch.csv --threads 3
+
+# 2023-07-31 17:01:10: example-batch/tyr_control.fq.gz is now processing...
+# 2023-07-31 17:01:16: Preprocess example-batch/tyr_control.fq.gz...
+# 2023-07-31 17:01:48: Output BAM files of example-batch/tyr_control.fq.gz...
+# 2023-07-31 17:01:52: 🍵 example-batch/tyr_control.fq.gz is finished!
+# 2023-07-31 17:01:52: example-batch/tyr_c230gt_50%.fq.gz is now processing...
+# 2023-07-31 17:01:52: example-batch/tyr_c230gt_10%.fq.gz is now processing...
+# 2023-07-31 17:01:52: example-batch/tyr_c230gt_01%.fq.gz is now processing...
+# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:02:17: Classify example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:02:19: Clustering example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:02:34: Classify example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:02:35: Classify example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:02:39: Clustering example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:02:39: Clustering example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:02:53: Consensus calling of example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:02:59: Output reports of example-batch/tyr_c230gt_50%.fq.gz...
+# 2023-07-31 17:03:04: 🍵 example-batch/tyr_c230gt_50%.fq.gz is finished!
+# 2023-07-31 17:03:39: Consensus calling of example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:03:51: Output reports of example-batch/tyr_c230gt_01%.fq.gz...
+# 2023-07-31 17:04:03: 🍵 example-batch/tyr_c230gt_01%.fq.gz is finished!
+# 2023-07-31 17:04:08: Consensus calling of example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:04:16: Output reports of example-batch/tyr_c230gt_10%.fq.gz...
+# 2023-07-31 17:04:24: 🍵 example-batch/tyr_c230gt_10%.fq.gz is finished!
+# 🎉 Finished! Open DAJIN_Results/tyr-substitution to see the report.
+```
+
+## 📈 Report Contents
+
+Upon completion of DAJIN2 processing, a directory named **DAJIN_Results** is generated.  
+Inside the **DAJIN_Results** directory, the following files can be found:  
+
+```
+DAJIN_Results/tyr-substitution
+├── BAM
+│   ├── tyr_c230gt_01%
+│   ├── tyr_c230gt_10%
+│   ├── tyr_c230gt_50%
+│   └── tyr_control
+├── FASTA
+│   ├── tyr_c230gt_01%
+│   ├── tyr_c230gt_10%
+│   └── tyr_c230gt_50%
+├── HTML
+│   ├── tyr_c230gt_01%
+│   ├── tyr_c230gt_10%
+│   └── tyr_c230gt_50%
+├── MUTATION_INFO
+│   ├── tyr_c230gt_01%.csv
+│   ├── tyr_c230gt_10%.csv
+│   └── tyr_c230gt_50%.csv
+├── read_all.csv
+├── read_plot.html
+├── read_plot.pdf
+└── read_summary.csv
+```
+
+### 1. BAM
+
+The BAM directory contains the BAM files of reads classified per allele.  
+
+> **Note**  
+> Specifying a reference genome using the `genome` option will align the reads to that genome.  
+> Without `genome` options, the reads will align to the control allele within the input FASTA file.
+
+### 2. FASTA and HTML
+
+The FASTA directory stores the FASTA files of each allele.  
+The HTML directory contains HTML files for each allele, where mutation sites are color-highlighted.  
+For example, Tyr point mutation is highlighted in **green**.  
+
+<img src="https://user-images.githubusercontent.com/15861316/274518501-2ca3f442-1b86-4635-be3d-fd37575c4ca2.png" width="75%" />
+
+### 3. MUTATION_INFO
+
+The MUTATION_INFO directory saves tables depicting mutation sites for each allele.  
+An example of a Tyr point mutation is described by its position on the chromosome and the type of mutation.  
+
+<img src="https://user-images.githubusercontent.com/15861316/274519342-a613490d-5dbb-4a27-a2cf-bca0686b30f0.png" width="75%">
+
+### 4. read_plot.html and read_plot.pdf
+
+Both read_plot.html and read_plot.pdf illustrate the proportions of each allele.  
+The chart's **Allele type** indicates the type of allele, and **% of reads** shows the proportion of reads for that allele.  
+
+Additionally, the types of **Allele type** include:
+- **intact**: Alleles that perfectly match the input FASTA allele.
+- **indels**: Substitutions, deletions, insertions, or inversions within 50 bases.
+- **sv**: Substitutions, deletions, insertions, or inversions beyond 50 bases.
+
+<img src="https://user-images.githubusercontent.com/15861316/274521067-4d217251-4c62-4dc9-9c05-7f5377dd3025.png" width="75%">
+
+> **Warning**  
+> In PCR amplicon sequencing, the % of reads might not match the actual allele proportions due to amplification bias.  
+> Especially when large deletions are present, the deletion alleles might be significantly amplified, potentially not reflecting the actual allele proportions.
+
+### 5. read_all.csv and read_summary.csv
+
+- read_all.csv: Records which allele each read is classified under.  
+- read_summary.csv: Describes the number of reads and presence proportion for each allele.  
+
+
+## 📄 References
+
+For more information, please refer to the following publication:
+
+[Kuno A, et al. (2022) DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes. *PLoS Biology* 20(1): e3001507.](https://doi.org/10.1371/journal.pbio.3001507)

DAJIN2-0.3.2/requirements.txt

@@ -0,0 +1,21 @@
+numpy >= 1.20.0
+scipy >=  1.6.0
+pandas >= 1.0.0
+openpyxl >= 3.0.0
+rapidfuzz >=3.0.0
+statsmodels >= 0.13.5
+scikit-learn >= 1.0.0
+
+mappy >= 2.24
+pysam >= 0.19.0
+
+Flask >= 2.2.0
+waitress >= 2.1.0
+Jinja2 >= 3.1.0
+
+plotly >= 5.0.0
+kaleido >= 0.2.0
+
+cstag >= 0.4.1
+midsv >= 0.10.1
+wslPath >=0.3.0

{DAJIN2-0.1.32a0 → DAJIN2-0.3.2}/setup.py

@@ -9,10 +9,10 @@ with open("requirements.txt") as requirements_file:
 
 setuptools.setup(
     name="DAJIN2",
-    version="0.1.32.alpha",
+    version="0.3.2",
     author="Akihiro Kuno",
     author_email="akuno@md.tsukuba.ac.jp",
-    description="One-step genotyping tools for Nanopore amplicon sequencing",
+    description="One-step genotyping tools for targeted long-read sequencing",
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/akikuno/DAJIN2",
@@ -21,12 +21,16 @@ setuptools.setup(
         where="src",
     ),
     package_dir={"": "src"},
-    entry_points={"console_scripts": ["DAJIN2=DAJIN2.DAJIN2:main"]},
+    entry_points={"console_scripts": ["DAJIN2=DAJIN2.main:execute"]},
     include_package_data=True,
     classifiers=[
+        "Development Status :: 4 - Beta",
+        "Environment :: Console",
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "Operating System :: POSIX",
+        "Operating System :: MacOS",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
-    python_requires=">=3.7",
 )

DAJIN2-0.3.2/src/DAJIN2/core/classification/__init__.py

@@ -0,0 +1 @@
+from DAJIN2.core.classification.classifier import classify_alleles

DAJIN2-0.3.2/src/DAJIN2/core/classification/classifier.py

@@ -0,0 +1,49 @@
+from __future__ import annotations
+
+import midsv
+from pathlib import Path
+from itertools import groupby
+
+
+def _calc_match(CSSPLIT: str) -> float:
+    match_score = CSSPLIT.count("=")
+    match_score -= CSSPLIT.count("+")  # insertion
+    match_score -= sum(cs.islower() for cs in CSSPLIT)  # inversion
+    cssplit = CSSPLIT.split(",")
+
+    return match_score / len(cssplit)
+
+
+def _score_allele(TEMPDIR: Path, allele: str, SAMPLE_NAME: str) -> list[dict]:
+    midsv_sample = midsv.read_jsonl(Path(TEMPDIR, SAMPLE_NAME, "midsv", f"{allele}.json"))
+    scored_alleles = []
+
+    for dict_midsv in midsv_sample:
+        score = _calc_match(dict_midsv["CSSPLIT"])
+        dict_midsv.update({"SCORE": score, "ALLELE": allele})
+        scored_alleles.append(dict_midsv)
+
+    return scored_alleles
+
+
+def _extract_alleles_with_max_score(score_of_each_alleles: list[dict]) -> list[dict]:
+    alleles_with_max_score = []
+    score_of_each_alleles.sort(key=lambda x: x["QNAME"])
+    for _, group in groupby(score_of_each_alleles, key=lambda x: x["QNAME"]):
+        max_read = max(group, key=lambda x: x["SCORE"])
+        del max_read["SCORE"]
+        alleles_with_max_score.append(max_read)
+    return alleles_with_max_score
+
+
+##########################################################
+# main
+##########################################################
+
+
+def classify_alleles(TEMPDIR: Path, FASTA_ALLELES: dict, SAMPLE_NAME: str) -> list[dict]:
+    score_of_each_alleles = []
+    for allele in FASTA_ALLELES:
+        score_of_each_alleles.extend(_score_allele(TEMPDIR, allele, SAMPLE_NAME))
+
+    return _extract_alleles_with_max_score(score_of_each_alleles)

DAJIN2-0.3.2/src/DAJIN2/core/clustering/__init__.py

@@ -0,0 +1,3 @@
+from DAJIN2.core.clustering.label_extractor import extract_labels
+from DAJIN2.core.clustering.appender import add_labels, add_readnum, add_percent
+from DAJIN2.core.clustering.label_handler import update_labels

DAJIN2-0.3.2/src/DAJIN2/core/clustering/appender.py

@@ -0,0 +1,44 @@
+from __future__ import annotations
+
+
+def add_labels(classif_sample: list[dict], labels: list[int]) -> list[dict]:
+    """Add 'LABEL' key to each sample dict, indicating each clster of allele."""
+    clust_sample = classif_sample.copy()
+
+    for clust, label in zip(clust_sample, labels):
+        clust["LABEL"] = label
+
+    return clust_sample
+
+
+def count_labels(clust_sample: list[dict]) -> dict[int, int]:
+    """Count the occurrences of each label in the cluster sample."""
+    label_count = {}
+    for sample in clust_sample:
+        label = sample["LABEL"]
+        label_count[label] = label_count.get(label, 0) + 1
+    return label_count
+
+
+def add_readnum(clust_sample: list[dict]) -> list[dict]:
+    """Add 'READNUM' key to each sample dict, indicating the number of occurrences of each label."""
+    clust_result = clust_sample.copy()
+    label_count = count_labels(clust_result)
+
+    for sample in clust_result:
+        sample["READNUM"] = label_count[sample["LABEL"]]
+
+    return clust_result
+
+
+def add_percent(clust_sample: list[dict]) -> list[dict]:
+    """Add 'PERCENT' key to each sample dict, indicating the percentage of occurrences of each label."""
+    clust_result = clust_sample.copy()
+    total_samples = len(clust_result)
+    label_count = count_labels(clust_result)
+
+    for sample in clust_result:
+        label = sample["LABEL"]
+        sample["PERCENT"] = round((label_count[label] / total_samples) * 100, 3)
+
+    return clust_result