DAJIN2 0.4.1__zip → 0.4.3__zip

{DAJIN2-0.4.1/src/DAJIN2.egg-info → DAJIN2-0.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DAJIN2
-Version: 0.4.1
+Version: 0.4.3
 Summary: One-step genotyping tools for targeted long-read sequencing
 Home-page: https://github.com/akikuno/DAJIN2
 Author: Akihiro Kuno
@@ -14,24 +14,22 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy>=1.20.0
-Requires-Dist: scipy>=1.6.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: scipy>=1.10.0
 Requires-Dist: pandas>=1.0.0
-Requires-Dist: openpyxl>=3.0.0
-Requires-Dist: rapidfuzz>=3.0.0
-Requires-Dist: statsmodels>=0.13.5
-Requires-Dist: scikit-learn>=1.0.0
-Requires-Dist: openpyxl>=3.0.0
+Requires-Dist: openpyxl>=3.1.0
+Requires-Dist: rapidfuzz>=3.6.0
+Requires-Dist: scikit-learn>=1.3.0
 Requires-Dist: mappy>=2.24
-Requires-Dist: pysam>=0.19.0
+Requires-Dist: pysam>=0.21.0
 Requires-Dist: Flask>=2.2.0
 Requires-Dist: waitress>=2.1.0
 Requires-Dist: Jinja2>=3.1.0
-Requires-Dist: plotly>=5.0.0
+Requires-Dist: plotly>=5.19.0
 Requires-Dist: kaleido>=0.2.0
-Requires-Dist: cstag>=0.4.1
-Requires-Dist: midsv>=0.10.1
-Requires-Dist: wslPath>=0.3.0
+Requires-Dist: cstag>=1.0.0
+Requires-Dist: midsv>=0.11.0
+Requires-Dist: wslPath>=0.4.1
 
 [![License](https://img.shields.io/badge/License-MIT-9cf.svg)](https://choosealicense.com/licenses/mit/)
 [![Test](https://img.shields.io/github/actions/workflow/status/akikuno/dajin2/pytest.yml?branch=main&label=Test&color=brightgreen)](https://github.com/akikuno/dajin2/actions)
@@ -56,14 +54,14 @@ The name DAJIN is derived from the phrase 一網**打尽** (Ichimou **DAJIN** or
 + **Comprehensive Mutation Detection**: Equipped with the capability to detect genome editing events over a wide range, it can identify a broad spectrum of mutations, from small changes to large structural variations.
   + DAJIN2 is also possible to detect complex mutations characteristic of genome editing, such as "insertions occurring in regions where deletions have occurred."
 + **Intuitive Visualization**: The outcomes of genome editing are visualized intuitively, allowing for the rapid and easy identification and analysis of mutations.
-+ **Multi-Sample Compatibility**: Accommodates a variety of samples, enabling simultaneous processing of multiple samples. This facilitates efficient progression of large-scale experiments and comparative studies.
++ **Multi-Sample Compatibility**: Enabling parallel processing of multiple samples. This facilitates efficient progression of large-scale experiments and comparative studies.
 
 
 ## 🛠 Installation
 
 ### Prerequisites
 
-- Python 3.7 or later
+- Python 3.8 or later
 - Unix-like environment (Linux, macOS, WSL2, etc.)
 
 ### From [Bioconda](https://anaconda.org/bioconda/DAJIN2) (Recommended)
@@ -80,6 +78,7 @@ conda activate env-dajin2
 > CONDA_SUBDIR=osx-64 conda create -n env-dajin2 -c conda-forge -c bioconda python=3.10 DAJIN2 -y
 > conda activate env-dajin2
 > conda config --env --set subdir osx-64
+> python -c "import platform; print(platform.machine())" # Confirm that the output is 'x86_64', not 'arm64'
 > ```
 
 ### From [PyPI](https://pypi.org/project/DAJIN2/)
@@ -92,7 +91,7 @@ pip install DAJIN2
 > If you encounter any issues during the installation, please refer to the [Troubleshooting Guide](https://github.com/akikuno/DAJIN2/blob/main/docs/TROUBLESHOOTING.md)
 
 
-## 💡 Usage
+## 💻 Usage
 
 ### Required Files
 
@@ -126,11 +125,11 @@ Assuming barcode01 as the control and barcode02 as the sample, specify each dire
 The FASTA file should contain descriptions of the alleles anticipated as a result of genome editing.
 
 > [!IMPORTANT]
-> Specifying the control allele: A header name >control and its sequence are mandatory.
+> **A header name >control and its sequence are mandatory.**
 
 If there are anticipated alleles (e.g., knock-ins or knock-outs), include their sequences in the FASTA file too. These anticipated alleles can be named arbitrarily.
 
-Below is a typical example of a FASTA file:
+Below is an example of a FASTA file:
 
 ```text
 >control
@@ -166,12 +165,17 @@ Options:
 #### Example
 
 ```bash
+# Download example dataset
+wget https://github.com/akikuno/DAJIN2/raw/main/examples/example_single.tar.gz
+tar -xf example_single.tar.gz
+
+# Run DAJIN2
 DAJIN2 \
-    --control example/barcode01 \
-    --sample example/barcode02 \
-    --allele example/design.fa \
-    --name IL6-knockin \
-    --genome hg38 \
+    --control example_single/control \
+    --sample example_single/sample \
+    --allele example_single/stx2_deletion.fa \
+    --name stx2_deletion \
+    --genome mm39 \
     --threads 4
 ```
 
@@ -208,7 +212,6 @@ DAJIN2 \
 
 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). -->
 
 > [!NOTE]
 > For guidance on how to compile sample information, please refer to [this document](https://docs.google.com/presentation/d/e/2PACX-1vSMEmXJPG2TNjfT66XZJRzqJd82aAqO5gJrdEzyhn15YBBr_Li-j5puOgVChYf3jA/embed?start=false&loop=false&delayms=3000).
@@ -226,13 +229,18 @@ options:
 #### Example
 
 ```bash
-DAJIN2 --file batch.csv --threads 4
+# 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 4
 ```
 
 <!-- ```bash
 # Donwload the example dataset
-wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-batch.tar.gz
-tar -xf example-batch.tar.gz
+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
@@ -313,16 +321,17 @@ For example, Tyr point mutation is highlighted in **green**.
 ### 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.  
+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
+### 4. resd_summary.xlsx, read_plot.html and read_plot.pdf
 
+read_summary.xlsx describes the number of reads and presence proportion for each allele.  
 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 **Percent of reads** shows the proportion of reads for that allele.  
+The chart's **Allele type** indicates the type of allele, and **Percent of reads** shows the proportion of reads for each allele.  
 
-Additionally, the types of **Allele type** include:
+The **Allele type** includes:
 - **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.
@@ -333,14 +342,10 @@ Additionally, the types of **Allele type** include:
 > 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_summary.xlsx
-
-- read_summary.xlsx: Describes the number of reads and presence proportion for each allele.  
-
 ## 📣Feedback and Support
 
 For questions, bug reports, or other forms of feedback, we'd love to hear from you!  
-Please use [GitHub Issues](https://github.com/akikuno/DAJIN2/issues) for all reporting purposes.  
+Please use [GitHub Issues](https://github.com/akikuno/DAJIN2/issues/new/choose) for all reporting purposes.  
 
 Please refer to [CONTRIBUTING](https://github.com/akikuno/DAJIN2/blob/main/docs/CONTRIBUTING.md) for how to contribute and how to verify your contributions.  
 

{DAJIN2-0.4.1 → DAJIN2-0.4.3}/README.md

@@ -21,14 +21,14 @@ The name DAJIN is derived from the phrase 一網**打尽** (Ichimou **DAJIN** or
 + **Comprehensive Mutation Detection**: Equipped with the capability to detect genome editing events over a wide range, it can identify a broad spectrum of mutations, from small changes to large structural variations.
   + DAJIN2 is also possible to detect complex mutations characteristic of genome editing, such as "insertions occurring in regions where deletions have occurred."
 + **Intuitive Visualization**: The outcomes of genome editing are visualized intuitively, allowing for the rapid and easy identification and analysis of mutations.
-+ **Multi-Sample Compatibility**: Accommodates a variety of samples, enabling simultaneous processing of multiple samples. This facilitates efficient progression of large-scale experiments and comparative studies.
++ **Multi-Sample Compatibility**: Enabling parallel processing of multiple samples. This facilitates efficient progression of large-scale experiments and comparative studies.
 
 
 ## 🛠 Installation
 
 ### Prerequisites
 
-- Python 3.7 or later
+- Python 3.8 or later
 - Unix-like environment (Linux, macOS, WSL2, etc.)
 
 ### From [Bioconda](https://anaconda.org/bioconda/DAJIN2) (Recommended)
@@ -45,6 +45,7 @@ conda activate env-dajin2
 > CONDA_SUBDIR=osx-64 conda create -n env-dajin2 -c conda-forge -c bioconda python=3.10 DAJIN2 -y
 > conda activate env-dajin2
 > conda config --env --set subdir osx-64
+> python -c "import platform; print(platform.machine())" # Confirm that the output is 'x86_64', not 'arm64'
 > ```
 
 ### From [PyPI](https://pypi.org/project/DAJIN2/)
@@ -57,7 +58,7 @@ pip install DAJIN2
 > If you encounter any issues during the installation, please refer to the [Troubleshooting Guide](https://github.com/akikuno/DAJIN2/blob/main/docs/TROUBLESHOOTING.md)
 
 
-## 💡 Usage
+## 💻 Usage
 
 ### Required Files
 
@@ -91,11 +92,11 @@ Assuming barcode01 as the control and barcode02 as the sample, specify each dire
 The FASTA file should contain descriptions of the alleles anticipated as a result of genome editing.
 
 > [!IMPORTANT]
-> Specifying the control allele: A header name >control and its sequence are mandatory.
+> **A header name >control and its sequence are mandatory.**
 
 If there are anticipated alleles (e.g., knock-ins or knock-outs), include their sequences in the FASTA file too. These anticipated alleles can be named arbitrarily.
 
-Below is a typical example of a FASTA file:
+Below is an example of a FASTA file:
 
 ```text
 >control
@@ -131,12 +132,17 @@ Options:
 #### Example
 
 ```bash
+# Download example dataset
+wget https://github.com/akikuno/DAJIN2/raw/main/examples/example_single.tar.gz
+tar -xf example_single.tar.gz
+
+# Run DAJIN2
 DAJIN2 \
-    --control example/barcode01 \
-    --sample example/barcode02 \
-    --allele example/design.fa \
-    --name IL6-knockin \
-    --genome hg38 \
+    --control example_single/control \
+    --sample example_single/sample \
+    --allele example_single/stx2_deletion.fa \
+    --name stx2_deletion \
+    --genome mm39 \
     --threads 4
 ```
 
@@ -173,7 +179,6 @@ DAJIN2 \
 
 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). -->
 
 > [!NOTE]
 > For guidance on how to compile sample information, please refer to [this document](https://docs.google.com/presentation/d/e/2PACX-1vSMEmXJPG2TNjfT66XZJRzqJd82aAqO5gJrdEzyhn15YBBr_Li-j5puOgVChYf3jA/embed?start=false&loop=false&delayms=3000).
@@ -191,13 +196,18 @@ options:
 #### Example
 
 ```bash
-DAJIN2 --file batch.csv --threads 4
+# 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 4
 ```
 
 <!-- ```bash
 # Donwload the example dataset
-wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-batch.tar.gz
-tar -xf example-batch.tar.gz
+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
@@ -278,16 +288,17 @@ For example, Tyr point mutation is highlighted in **green**.
 ### 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.  
+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
+### 4. resd_summary.xlsx, read_plot.html and read_plot.pdf
 
+read_summary.xlsx describes the number of reads and presence proportion for each allele.  
 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 **Percent of reads** shows the proportion of reads for that allele.  
+The chart's **Allele type** indicates the type of allele, and **Percent of reads** shows the proportion of reads for each allele.  
 
-Additionally, the types of **Allele type** include:
+The **Allele type** includes:
 - **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.
@@ -298,14 +309,10 @@ Additionally, the types of **Allele type** include:
 > 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_summary.xlsx
-
-- read_summary.xlsx: Describes the number of reads and presence proportion for each allele.  
-
 ## 📣Feedback and Support
 
 For questions, bug reports, or other forms of feedback, we'd love to hear from you!  
-Please use [GitHub Issues](https://github.com/akikuno/DAJIN2/issues) for all reporting purposes.  
+Please use [GitHub Issues](https://github.com/akikuno/DAJIN2/issues/new/choose) for all reporting purposes.  
 
 Please refer to [CONTRIBUTING](https://github.com/akikuno/DAJIN2/blob/main/docs/CONTRIBUTING.md) for how to contribute and how to verify your contributions.  
 

DAJIN2-0.4.3/requirements.txt

@@ -0,0 +1,20 @@
+numpy >= 1.24.0
+scipy >= 1.10.0
+pandas >= 1.0.0
+openpyxl >= 3.1.0
+rapidfuzz >=3.6.0
+scikit-learn >= 1.3.0
+
+mappy >= 2.24
+pysam >= 0.21.0
+
+Flask >= 2.2.0
+waitress >= 2.1.0
+Jinja2 >= 3.1.0
+
+plotly >= 5.19.0
+kaleido >= 0.2.0
+
+cstag >= 1.0.0
+midsv >= 0.11.0
+wslPath >=0.4.1

{DAJIN2-0.4.1 → DAJIN2-0.4.3}/setup.py

@@ -9,7 +9,7 @@ with open("requirements.txt") as requirements_file:
 
 setuptools.setup(
     name="DAJIN2",
-    version="0.4.1",
+    version="0.4.3",
     author="Akihiro Kuno",
     author_email="akuno@md.tsukuba.ac.jp",
     description="One-step genotyping tools for targeted long-read sequencing",

{DAJIN2-0.4.1 → DAJIN2-0.4.3}/src/DAJIN2/core/clustering/label_merger.py

@@ -11,20 +11,6 @@ def calculate_label_percentages(labels: list[int]) -> dict[int, float]:
     return {label: (count / total_labels * 100) for label, count in label_counts.items()}
 
 
-def merge_mixed_cluster(labels_control: list[int], labels_sample: list[int], threshold: float = 0.5) -> list[int]:
-    """Merge labels in sample if they appear more than 'threshold' percentage in control."""
-    labels_merged = labels_sample.copy()
-    label_percentages_control = calculate_label_percentages(labels_control)
-    mixed_labels = {label for label, percent in label_percentages_control.items() if percent > threshold}
-
-    new_label = max(labels_merged) + 1
-    for i, label in enumerate(labels_sample):
-        if label in mixed_labels:
-            labels_merged[i] = new_label
-
-    return labels_merged
-
-
 def map_clusters_to_previous(labels_sample: list[int], labels_previous: list[int]) -> dict[int, int]:
     """
     Determine which cluster in labels_previous corresponds to each cluster in labels_sample.
@@ -63,6 +49,8 @@ def merge_minor_cluster(
     minor_labels_percentage = {label for label, percent in label_percentages.items() if percent < threshold_percentage}
     minor_labels_readnumber = {label for label, num in Counter(labels_sample).items() if num <= threshold_readnumber}
     minor_labels = minor_labels_percentage | minor_labels_readnumber
+    if minor_labels == set():
+        return labels_sample
 
     correspondence = map_clusters_to_previous(labels_sample, labels_previous)
     update_required_labels = get_update_required_labels(correspondence)
@@ -70,7 +58,23 @@ def merge_minor_cluster(
     labels_merged = labels_sample.copy()
     for m in minor_labels:
         new_label = max(labels_merged) + 1
-        labels_merged = [new_label if label in update_required_labels[correspondence[m]] else label for label in labels_merged]
+        labels_merged = [
+            new_label if label in update_required_labels[correspondence[m]] else label for label in labels_merged
+        ]
+
+    return labels_merged
+
+
+def merge_mixed_cluster(labels_control: list[int], labels_sample: list[int], threshold: float = 0.5) -> list[int]:
+    """Merge labels in sample if they appear more than 'threshold' percentage in control."""
+    labels_merged = labels_sample.copy()
+    label_percentages_control = calculate_label_percentages(labels_control)
+    mixed_labels = {label for label, percent in label_percentages_control.items() if percent > threshold}
+
+    new_label = max(labels_merged) + 1
+    for i, label in enumerate(labels_sample):
+        if label in mixed_labels:
+            labels_merged[i] = new_label
 
     return labels_merged
 
@@ -82,7 +86,7 @@ def merge_minor_cluster(
 
 def merge_labels(labels_control: list[int], labels_sample: list[int], labels_previous: list[int]) -> list[int]:
     labels_merged = merge_minor_cluster(
-        labels_sample, labels_previous, threshold_percentage=0.5, threshold_readnumber=10
+        labels_sample, labels_previous, threshold_percentage=0.5, threshold_readnumber=5
     )
     labels_merged = merge_mixed_cluster(labels_control, labels_merged)
     return labels_merged

{DAJIN2-0.4.1 → DAJIN2-0.4.3}/src/DAJIN2/core/consensus/consensus.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import NamedTuple
+from dataclasses import dataclass
 from itertools import groupby
 from collections import defaultdict
 
@@ -90,7 +90,8 @@ def call_percentage(cssplits: list[list[str]], mutation_loci: list[set[str]]) ->
 ###########################################################
 
 
-class ConsensusKey(NamedTuple):
+@dataclass(frozen=True)
+class ConsensusKey:
     allele: str
     label: int
     percent: float

{DAJIN2-0.4.1 → DAJIN2-0.4.3}/src/DAJIN2/core/consensus/name_handler.py

@@ -1,13 +1,7 @@
 from __future__ import annotations
 
 import re
-from typing import NamedTuple
-
-
-class ConsensusKey(NamedTuple):
-    allele: str
-    label: int
-    percent: float
+from DAJIN2.core.consensus.consensus import ConsensusKey
 
 
 def _detect_sv(cons_percentages: dict[ConsensusKey, list], threshold: int = 50) -> list[bool]:

{DAJIN2-0.4.1 → DAJIN2-0.4.3}/src/DAJIN2/core/core.py

@@ -2,119 +2,16 @@ from __future__ import annotations
 
 import shutil
 import logging
-import uuid
 
 from pathlib import Path
-from typing import NamedTuple
-from collections import defaultdict
 
-from DAJIN2.utils import io, config, fastx_handler
+from DAJIN2.utils import io, fastx_handler
 from DAJIN2.core import classification, clustering, consensus, preprocess, report
+from DAJIN2.core.preprocess.input_formatter import FormattedInputs
 
 logger = logging.getLogger(__name__)
 
 
-def parse_arguments(arguments: dict) -> tuple:
-    genome_urls = defaultdict(str)
-    if arguments.get("genome"):
-        genome_urls.update(
-            {"genome": arguments["genome"], "blat": arguments["blat"], "goldenpath": arguments["goldenpath"]}
-        )
-
-    return (
-        arguments["sample"],
-        arguments["control"],
-        arguments["allele"],
-        arguments["name"],
-        arguments["threads"],
-        genome_urls,
-        uuid.uuid4().hex,
-    )
-
-
-def convert_input_paths_to_posix(sample: str, control: str, allele: str) -> tuple:
-    sample = io.convert_to_posix(sample)
-    control = io.convert_to_posix(control)
-    allele = io.convert_to_posix(allele)
-
-    return sample, control, allele
-
-
-def create_temporal_directory(name: str, control_name: str) -> Path:
-    tempdir = Path(config.TEMP_ROOT_DIR, name)
-    Path(tempdir, "cache", ".igvjs", control_name).mkdir(parents=True, exist_ok=True)
-
-    return tempdir
-
-
-def check_caches(tempdir: Path, path_allele: str, genome_url: str) -> bool:
-    is_cache_hash = preprocess.cache_checker.exists_cached_hash(tempdir=tempdir, path=path_allele)
-    is_cache_genome = preprocess.cache_checker.exists_cached_genome(tempdir=tempdir, genome=genome_url)
-
-    return is_cache_hash and is_cache_genome
-
-
-def get_genome_coordinates(genome_urls: dict, fasta_alleles: dict, is_cache_genome: bool, tempdir: Path) -> dict:
-    genome_coordinates = {
-        "genome": genome_urls["genome"],
-        "chrom_size": 0,
-        "chrom": "control",
-        "start": 0,
-        "end": len(fasta_alleles["control"]) - 1,
-        "strand": "+",
-    }
-    if genome_urls["genome"]:
-        if is_cache_genome:
-            genome_coordinates = next(io.read_jsonl(Path(tempdir, "cache", "genome_coordinates.jsonl")))
-        else:
-            genome_coordinates = preprocess.genome_fetcher.fetch_coordinates(
-                genome_coordinates, genome_urls, fasta_alleles["control"]
-            )
-            genome_coordinates["chrom_size"] = preprocess.genome_fetcher.fetch_chromosome_size(
-                genome_coordinates, genome_urls
-            )
-            io.write_jsonl([genome_coordinates], Path(tempdir, "cache", "genome_coordinates.jsonl"))
-
-    return genome_coordinates
-
-
-class FormattedInputs(NamedTuple):
-    path_sample: str
-    path_control: str
-    path_allele: str
-    sample_name: str
-    control_name: str
-    fasta_alleles: dict[str, str]
-    tempdir: Path
-    genome_coordinates: dict[str, str]
-    threads: int
-    uuid: str
-
-
-def format_inputs(arguments: dict) -> FormattedInputs:
-    path_sample, path_control, path_allele, name, threads, genome_urls, uuid = parse_arguments(arguments)
-    path_sample, path_control, path_allele = convert_input_paths_to_posix(path_sample, path_control, path_allele)
-    sample_name = preprocess.fastx_parser.extract_basename(path_sample)
-    control_name = preprocess.fastx_parser.extract_basename(path_control)
-    fasta_alleles = preprocess.fastx_parser.dictionize_allele(path_allele)
-    tempdir = create_temporal_directory(name, control_name)
-    is_cache_genome = check_caches(tempdir, path_allele, genome_urls["genome"])
-    genome_coordinates = get_genome_coordinates(genome_urls, fasta_alleles, is_cache_genome, tempdir)
-
-    return FormattedInputs(
-        path_sample,
-        path_control,
-        path_allele,
-        sample_name,
-        control_name,
-        fasta_alleles,
-        tempdir,
-        genome_coordinates,
-        threads,
-        uuid,
-    )
-
-
 ###########################################################
 # main
 ###########################################################
@@ -126,9 +23,9 @@ def execute_control(arguments: dict):
     ###########################################################
     # Preprocess
     ###########################################################
-    ARGS = format_inputs(arguments)
-    preprocess.directories.create_temporal_directories(ARGS.tempdir, ARGS.control_name, is_control=True)
-    preprocess.directories.create_report_directories(ARGS.tempdir, ARGS.control_name, is_control=True)
+    ARGS: FormattedInputs = preprocess.format_inputs(arguments)
+    preprocess.create_temporal_directories(ARGS.tempdir, ARGS.control_name, is_control=True)
+    preprocess.create_report_directories(ARGS.tempdir, ARGS.control_name, is_control=True)
     io.cache_control_hash(ARGS.tempdir, ARGS.path_allele)
 
     ###########################################################
@@ -151,7 +48,7 @@ def execute_control(arguments: dict):
     # ============================================================
     # Export fasta files as single-FASTA format
     # ============================================================
-    preprocess.fastx_parser.export_fasta_files(ARGS.tempdir, ARGS.fasta_alleles, ARGS.control_name)
+    fastx_handler.export_fasta_files(ARGS.tempdir, ARGS.fasta_alleles, ARGS.control_name)
 
     # ============================================================
     # Mapping using mappy
@@ -173,8 +70,8 @@ def execute_control(arguments: dict):
     # Output BAM files
     ###########################################################
     logger.info(f"Output BAM files of {arguments['control']}...")
-    report.report_bam.export_to_bam(
-        ARGS.tempdir, ARGS.control_name, ARGS.genome_coordinates, ARGS.threads, is_control=True
+    report.bam_exporter.export_to_bam(
+        ARGS.tempdir, ARGS.control_name, ARGS.genome_coordinates, ARGS.threads, ARGS.uuid, is_control=True
     )
     ###########################################################
     # Finish call
@@ -189,9 +86,9 @@ def execute_sample(arguments: dict):
     # Preprocess
     ###########################################################
 
-    ARGS = format_inputs(arguments)
-    preprocess.directories.create_temporal_directories(ARGS.tempdir, ARGS.sample_name, is_control=False)
-    preprocess.directories.create_report_directories(ARGS.tempdir, ARGS.sample_name, is_control=False)
+    ARGS: FormattedInputs = preprocess.format_inputs(arguments)
+    preprocess.create_temporal_directories(ARGS.tempdir, ARGS.sample_name, is_control=False)
+    preprocess.create_report_directories(ARGS.tempdir, ARGS.sample_name, is_control=False)
 
     logger.info(f"Preprocess {arguments['sample']}...")
 
@@ -209,7 +106,7 @@ def execute_sample(arguments: dict):
         shutil.copy(path_fasta, Path(ARGS.tempdir, ARGS.sample_name, "fasta"))
 
     paths_fasta = Path(ARGS.tempdir, ARGS.sample_name, "fasta").glob("*.fasta")
-    preprocess.mapping.generate_sam(ARGS, paths_fasta, is_control=False, is_insertion=False)
+    preprocess.generate_sam(ARGS, paths_fasta, is_control=False, is_insertion=False)
 
     # ============================================================
     # MIDSV conversion
@@ -234,8 +131,8 @@ def execute_sample(arguments: dict):
 
     if paths_insertion_fasta:
         # mapping to insertion alleles
-        preprocess.mapping.generate_sam(ARGS, paths_insertion_fasta, is_control=True, is_insertion=True)
-        preprocess.mapping.generate_sam(ARGS, paths_insertion_fasta, is_control=False, is_insertion=True)
+        preprocess.generate_sam(ARGS, paths_insertion_fasta, is_control=True, is_insertion=True)
+        preprocess.generate_sam(ARGS, paths_insertion_fasta, is_control=False, is_insertion=True)
         # add insertions to ARGS.fasta_alleles
         for path_fasta in paths_insertion_fasta:
             allele, seq = Path(path_fasta).read_text().strip().split("\n")
@@ -307,15 +204,15 @@ def execute_sample(arguments: dict):
     # RESULT
     io.write_jsonl(RESULT_SAMPLE, Path(ARGS.tempdir, "result", f"{ARGS.sample_name}.jsonl"))
     # FASTA
-    report.report_files.export_to_fasta(ARGS.tempdir, ARGS.sample_name, cons_sequence)
-    report.report_files.export_reference_to_fasta(ARGS.tempdir, ARGS.sample_name)
+    report.sequence_exporter.export_to_fasta(ARGS.tempdir, ARGS.sample_name, cons_sequence)
+    report.sequence_exporter.export_reference_to_fasta(ARGS.tempdir, ARGS.sample_name)
     # HTML
-    report.report_files.export_to_html(ARGS.tempdir, ARGS.sample_name, cons_percentage)
+    report.sequence_exporter.export_to_html(ARGS.tempdir, ARGS.sample_name, cons_percentage)
     # CSV (Allele Info)
-    report.report_mutation.export_to_csv(ARGS.tempdir, ARGS.sample_name, ARGS.genome_coordinates, cons_percentage)
+    report.mutation_exporter.export_to_csv(ARGS.tempdir, ARGS.sample_name, ARGS.genome_coordinates, cons_percentage)
     # BAM
-    report.report_bam.export_to_bam(
-        ARGS.tempdir, ARGS.sample_name, ARGS.genome_coordinates, ARGS.threads, RESULT_SAMPLE
+    report.bam_exporter.export_to_bam(
+        ARGS.tempdir, ARGS.sample_name, ARGS.genome_coordinates, ARGS.threads, ARGS.uuid, RESULT_SAMPLE
     )
     for path_bam_igvjs in Path(ARGS.tempdir, "cache", ".igvjs").glob(f"{ARGS.control_name}_control.bam*"):
         shutil.copy(path_bam_igvjs, Path(ARGS.tempdir, "report", ".igvjs", ARGS.sample_name))

DAJIN2-0.4.3/src/DAJIN2/core/preprocess/__init__.py

@@ -0,0 +1,9 @@
+from DAJIN2.core.preprocess.cache_checker import exists_cached_hash, exists_cached_genome
+from DAJIN2.core.preprocess.genome_fetcher import fetch_coordinates, fetch_chromosome_size
+from DAJIN2.core.preprocess.mapping import generate_sam
+from DAJIN2.core.preprocess.directory_manager import create_temporal_directories, create_report_directories
+from DAJIN2.core.preprocess.input_formatter import format_inputs
+from DAJIN2.core.preprocess.midsv_caller import generate_midsv
+from DAJIN2.core.preprocess.knockin_handler import extract_knockin_loci
+from DAJIN2.core.preprocess.mutation_extractor import cache_mutation_loci
+from DAJIN2.core.preprocess.insertions_to_fasta import generate_insertion_fasta