DAJIN2 0.4.1__zip → 0.4.2__zip

{DAJIN2-0.4.1/src/DAJIN2.egg-info → DAJIN2-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DAJIN2
-Version: 0.4.1
+Version: 0.4.2
 Summary: One-step genotyping tools for targeted long-read sequencing
 Home-page: https://github.com/akikuno/DAJIN2
 Author: Akihiro Kuno
@@ -19,9 +19,7 @@ Requires-Dist: scipy>=1.6.0
 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: mappy>=2.24
 Requires-Dist: pysam>=0.19.0
 Requires-Dist: Flask>=2.2.0
@@ -29,7 +27,7 @@ Requires-Dist: waitress>=2.1.0
 Requires-Dist: Jinja2>=3.1.0
 Requires-Dist: plotly>=5.0.0
 Requires-Dist: kaleido>=0.2.0
-Requires-Dist: cstag>=0.4.1
+Requires-Dist: cstag>=1.0.0
 Requires-Dist: midsv>=0.10.1
 Requires-Dist: wslPath>=0.3.0
 
@@ -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)
@@ -92,7 +90,7 @@ 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 +124,11 @@ 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
@@ -313,16 +311,17 @@ 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 +332,10 @@ 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 → DAJIN2-0.4.2}/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)
@@ -57,7 +57,7 @@ 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 +91,11 @@ 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
@@ -278,16 +278,17 @@ 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 +299,10 @@ 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 → DAJIN2-0.4.2}/requirements.txt

@@ -3,11 +3,8 @@ 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
 
-openpyxl >= 3.0.0
-
 mappy >= 2.24
 pysam >= 0.19.0
 
@@ -18,6 +15,6 @@ Jinja2 >= 3.1.0
 plotly >= 5.0.0
 kaleido >= 0.2.0
 
-cstag >= 0.4.1
+cstag >= 1.0.0
 midsv >= 0.10.1
 wslPath >=0.3.0

{DAJIN2-0.4.1 → DAJIN2-0.4.2}/setup.py

@@ -9,7 +9,7 @@ with open("requirements.txt") as requirements_file:
 
 setuptools.setup(
     name="DAJIN2",
-    version="0.4.1",
+    version="0.4.2",
     author="Akihiro Kuno",
     author_email="akuno@md.tsukuba.ac.jp",
     description="One-step genotyping tools for targeted long-read sequencing",

{DAJIN2-0.4.1 → DAJIN2-0.4.2}/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 → DAJIN2-0.4.2}/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 → DAJIN2-0.4.2}/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
@@ -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")

DAJIN2-0.4.2/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

DAJIN2-0.4.2/src/DAJIN2/core/preprocess/input_formatter.py

@@ -0,0 +1,109 @@
+from __future__ import annotations
+
+import uuid
+
+from pathlib import Path
+from dataclasses import dataclass
+from collections import defaultdict
+
+from DAJIN2.utils import io, config, fastx_handler
+
+from DAJIN2.core import preprocess
+
+
+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.exists_cached_hash(tempdir=tempdir, path=path_allele)
+    is_cache_genome = preprocess.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.fetch_coordinates(genome_coordinates, genome_urls, fasta_alleles["control"])
+            genome_coordinates["chrom_size"] = preprocess.fetch_chromosome_size(genome_coordinates, genome_urls)
+            io.write_jsonl([genome_coordinates], Path(tempdir, "cache", "genome_coordinates.jsonl"))
+
+    return genome_coordinates
+
+
+@dataclass(frozen=True)
+class FormattedInputs:
+    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 = fastx_handler.extract_filename(path_sample)
+    control_name = fastx_handler.extract_filename(path_control)
+    fasta_alleles = fastx_handler.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,
+    )

{DAJIN2-0.4.1 → DAJIN2-0.4.2}/src/DAJIN2/core/preprocess/mapping.py

@@ -43,6 +43,10 @@ def to_sam(
             query_seq = QUERY_SEQ.upper()
             query_qual = QUERY_QUAL
 
+            # Skip multi-mapping reads
+            if hit.mapq == 0:
+                continue
+
             # Report flag
             if hit.is_primary:
                 flag = 0 if hit.strand == 1 else 16

{DAJIN2-0.4.1 → DAJIN2-0.4.2}/src/DAJIN2/core/preprocess/midsv_caller.py

@@ -215,8 +215,8 @@ def generate_midsv(ARGS, is_control: bool = False, is_insertion: bool = False) -
             path_splice = Path(ARGS.tempdir, name, "sam", f"splice_{allele}.sam")
             path_output_midsv = Path(ARGS.tempdir, name, "midsv", f"{allele}.json")
 
-        sam_ont = sam_handler.remove_overlapped_reads(list(midsv.read_sam(path_ont)))
-        sam_splice = sam_handler.remove_overlapped_reads(list(midsv.read_sam(path_splice)))
+        sam_ont = sam_handler.remove_overlapped_reads(list(sam_handler.read_sam(path_ont)))
+        sam_splice = sam_handler.remove_overlapped_reads(list(sam_handler.read_sam(path_splice)))
         qname_of_map_ont = extract_qname_of_map_ont(sam_ont, sam_splice)
         sam_of_map_ont = filter_sam_by_preset(sam_ont, qname_of_map_ont, preset="map-ont")
         sam_of_splice = filter_sam_by_preset(sam_splice, qname_of_map_ont, preset="splice")

{DAJIN2-0.4.1 → DAJIN2-0.4.2}/src/DAJIN2/main.py

@@ -20,7 +20,7 @@ from DAJIN2.core import core
 from DAJIN2.utils import io, config, report_generator, input_validator, multiprocess
 
 
-DAJIN_VERSION = "0.4.1"
+DAJIN_VERSION = "0.4.2"
 
 
 def generate_report(name: str) -> None:

DAJIN2-0.4.2/src/DAJIN2/utils/fastx_handler.py

@@ -0,0 +1,94 @@
+from __future__ import annotations
+
+import re
+import gzip
+from pathlib import Path
+
+import mappy
+
+
+#################################################
+# Helper function
+#################################################
+
+
+def sanitize_filename(path_file: Path | str) -> str:
+    """
+    Sanitize the path_file by replacing invalid characters on Windows OS with '-'
+    """
+    path_file = str(path_file).lstrip()
+    if not path_file:
+        raise ValueError("Provided FASTA/FASTQ is empty or consists only of whitespace")
+    return re.sub(r'[\\/:?.,\'"<>| ]', "-", path_file)
+
+
+#################################################
+# Extract filename
+#################################################
+
+
+def extract_filename(path_fasta: Path | str) -> str:
+    filename = Path(path_fasta).name
+    filename = re.sub(r"\..*$", "", filename)  # Remove file extension
+    return sanitize_filename(filename)
+
+
+#################################################
+# Convert allele file to dictionary type fasta format
+#################################################
+
+
+def dictionize_allele(path_fasta: str | Path) -> dict[str, str]:
+    return {sanitize_filename(name): seq.upper() for name, seq, _ in mappy.fastx_read(str(path_fasta))}
+
+
+#################################################
+# Export fasta files as single-FASTA format
+#################################################
+
+
+def export_fasta_files(TEMPDIR: Path, FASTA_ALLELES: dict, NAME: str) -> None:
+    """+ Save multiple FASTAs in separate single-FASTA format files."""
+    for identifier, sequence in FASTA_ALLELES.items():
+        contents = "\n".join([">" + identifier, sequence]) + "\n"
+        output_fasta = Path(TEMPDIR, NAME, "fasta", f"{identifier}.fasta")
+        output_fasta.write_text(contents)
+
+
+#################################################
+# save_concatenated_fastx
+#################################################
+
+
+def extract_extention(path_file: Path) -> str:
+    suffixes = path_file.suffixes
+    return "".join(suffixes)
+
+
+def is_gzip_file(path_file: Path) -> bool:
+    """Check if a file is a GZip compressed file."""
+    try:
+        with path_file.open("rb") as f:
+            return f.read(2) == b"\x1f\x8b"
+    except IOError:
+        return False
+
+
+def save_fastq_as_gzip(TEMPDIR: Path, path_fastx: list[Path], barcode: str) -> None:
+    """Merge gzip and non-gzip files into a single gzip file."""
+    with gzip.open(Path(TEMPDIR, barcode, "fastq", f"{barcode}.fastq.gz"), "wb") as merged_file:
+        for path_file in path_fastx:
+            if is_gzip_file(path_file):
+                with gzip.open(path_file, "rb") as f:
+                    merged_file.write(f.read())
+            else:
+                with open(path_file, "r") as f:
+                    merged_file.write(f.read().encode())
+
+
+def save_concatenated_fastx(TEMPDIR: Path, directory: str) -> None:
+    fastx_suffix = {".fa", ".fq", ".fasta", ".fastq", ".fa.gz", ".fq.gz", ".fasta.gz", ".fastq.gz"}
+    path_directory = Path(directory)
+    barcode = path_directory.stem
+    path_fastx = [path for path in path_directory.iterdir() if extract_extention(path) in fastx_suffix]
+    save_fastq_as_gzip(TEMPDIR, path_fastx, barcode)

{DAJIN2-0.4.1 → DAJIN2-0.4.2}/src/DAJIN2/utils/input_validator.py

@@ -23,40 +23,51 @@ def update_threads(threads: int) -> int:
 ########################################################################
 
 
-def validate_file_existence(input_file: str):
-    if not Path(input_file).exists():
-        raise FileNotFoundError(f"{input_file} is not found")
+def validate_file_existence(path_file: str):
+    if not Path(path_file).exists():
+        raise FileNotFoundError(f"{path_file} is not found")
 
 
-def validate_fastq_extension(fastq_path: str):
-    if not re.search(r".fastq$|.fastq.gz$|.fq$|.fq.gz$", fastq_path):
-        raise ValueError(f"{fastq_path} requires extensions either 'fastq', 'fastq.gz', 'fq' or 'fq.gz'")
+def validate_fastq_extension(path_fastq: str):
+    if not re.search(r".fastq$|.fastq.gz$|.fq$|.fq.gz$", path_fastq):
+        raise ValueError(f"{path_fastq} requires extensions either 'fastq', 'fastq.gz', 'fq' or 'fq.gz'")
 
 
-# Varidate if the file is in the proper format.
-# See top 100 lines
-def validate_fastq_content(fastq_path: str):
+# Varidate if the file is in the proper format viewing top 100 lines
+def validate_fastq_content(path_fastq: str):
     try:
-        names, seqs, quals = zip(*[(n, s, q) for i, (n, s, q) in enumerate(mappy.fastx_read(fastq_path)) if i < 100])
-        if not (len(names) == len(seqs) == len(quals) > 0):
+        headers, seqs, quals = zip(*[(n, s, q) for i, (n, s, q) in enumerate(mappy.fastx_read(path_fastq)) if i < 100])
+        # Remove empty elements
+        headers = [header for header in headers if header]
+        seqs = [seq for seq in seqs if seq]
+        quals = [qual for qual in quals if qual]
+
+        if not (len(headers) == len(seqs) == len(quals) > 0):
             raise ValueError
+
     except ValueError:
-        raise ValueError(f"{fastq_path} is not a FASTQ format")
+        raise ValueError(f"{path_fastq} is not a proper FASTQ format")
 
 
-def validate_fasta_content(fasta_path: str):
+def validate_fasta_content(path_fasta: str):
     try:
-        names, seqs = zip(*[(n, s) for n, s, _ in mappy.fastx_read(fasta_path)])
-        if len(names) != len(seqs) or not names:
+        headers, seqs = zip(*[(n, s) for n, s, _ in mappy.fastx_read(path_fasta)])
+        # Remove empty elements
+        headers = [header for header in headers if header]
+        seqs = [seq for seq in seqs if seq]
+
+        if len(headers) != len(seqs) or not headers:
             raise ValueError
+
     except ValueError:
-        raise ValueError(f"{fasta_path} is not a proper FASTA format")
-    if len(names) != len(set(names)):
-        raise ValueError(f"{fasta_path} must include unique identifiers")
+        raise ValueError(f"{path_fasta} is not a proper FASTA format")
+
+    if len(headers) != len(set(headers)):
+        raise ValueError(f"{path_fasta} must include unique identifiers")
     if len(seqs) != len(set(seqs)):
-        raise ValueError(f"{fasta_path} must include unique DNA sequences")
-    if "control" not in names:
-        raise ValueError(f"One of the headers in the {fasta_path} must be '>control'")
+        raise ValueError(f"{path_fasta} must include unique DNA sequences")
+    if "control" not in headers:
+        raise ValueError(f"One of the headers in the {path_fasta} must be '>control'")
 
 
 def validate_files(SAMPLE: str, CONTROL: str, ALLELE: str) -> None:

{DAJIN2-0.4.1 → DAJIN2-0.4.2}/src/DAJIN2/utils/sam_handler.py

@@ -1,6 +1,9 @@
 from __future__ import annotations
 
 import re
+
+from pathlib import Path
+from typing import Generator
 from itertools import groupby
 from DAJIN2.utils.dna_handler import revcomp
 
@@ -22,6 +25,17 @@ def is_mapped(s: list[str]) -> bool:
     return not s[0].startswith("@") and s[9] != "*"
 
 
+###########################################################
+# Read sam
+###########################################################
+
+
+def read_sam(path_of_sam: str | Path) -> Generator[list]:
+    with open(path_of_sam) as f:
+        for line in f:
+            yield line.strip().split("\t")
+
+
 ###########################################################
 # remove_overlapped_reads
 ###########################################################

{DAJIN2-0.4.1 → DAJIN2-0.4.2/src/DAJIN2.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: DAJIN2
-Version: 0.4.1
+Version: 0.4.2
 Summary: One-step genotyping tools for targeted long-read sequencing
 Home-page: https://github.com/akikuno/DAJIN2
 Author: Akihiro Kuno
@@ -19,9 +19,7 @@ Requires-Dist: scipy>=1.6.0
 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: mappy>=2.24
 Requires-Dist: pysam>=0.19.0
 Requires-Dist: Flask>=2.2.0
@@ -29,7 +27,7 @@ Requires-Dist: waitress>=2.1.0
 Requires-Dist: Jinja2>=3.1.0
 Requires-Dist: plotly>=5.0.0
 Requires-Dist: kaleido>=0.2.0
-Requires-Dist: cstag>=0.4.1
+Requires-Dist: cstag>=1.0.0
 Requires-Dist: midsv>=0.10.1
 Requires-Dist: wslPath>=0.3.0
 
@@ -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)
@@ -92,7 +90,7 @@ 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 +124,11 @@ 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
@@ -313,16 +311,17 @@ 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 +332,10 @@ 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 → DAJIN2-0.4.2}/src/DAJIN2.egg-info/SOURCES.txt

@@ -36,10 +36,10 @@ src/DAJIN2/core/consensus/name_handler.py
 src/DAJIN2/core/consensus/similarity_searcher.py
 src/DAJIN2/core/preprocess/__init__.py
 src/DAJIN2/core/preprocess/cache_checker.py
-src/DAJIN2/core/preprocess/directories.py
-src/DAJIN2/core/preprocess/fastx_parser.py
+src/DAJIN2/core/preprocess/directory_manager.py
 src/DAJIN2/core/preprocess/genome_fetcher.py
 src/DAJIN2/core/preprocess/homopolymer_handler.py
+src/DAJIN2/core/preprocess/input_formatter.py
 src/DAJIN2/core/preprocess/insertions_to_fasta.py
 src/DAJIN2/core/preprocess/knockin_handler.py
 src/DAJIN2/core/preprocess/mapping.py

{DAJIN2-0.4.1 → DAJIN2-0.4.2}/src/DAJIN2.egg-info/requires.txt

@@ -3,9 +3,7 @@ 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
-openpyxl>=3.0.0
 mappy>=2.24
 pysam>=0.19.0
 Flask>=2.2.0
@@ -13,6 +11,6 @@ waitress>=2.1.0
 Jinja2>=3.1.0
 plotly>=5.0.0
 kaleido>=0.2.0
-cstag>=0.4.1
+cstag>=1.0.0
 midsv>=0.10.1
 wslPath>=0.3.0

DAJIN2-0.4.1/src/DAJIN2/core/preprocess/__init__.py

@@ -1,12 +0,0 @@
-from DAJIN2.core.preprocess import (
-    fastx_parser,
-    genome_fetcher,
-    cache_checker,
-    directories,
-)
-
-from DAJIN2.core.preprocess.mapping import generate_sam
-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

DAJIN2-0.4.1/src/DAJIN2/core/preprocess/fastx_parser.py

@@ -1,59 +0,0 @@
-from __future__ import annotations
-
-import re
-from pathlib import Path
-
-import mappy
-
-########################################################################
-# Helper function
-########################################################################
-
-
-def _sanitize_name(name: str) -> str:
-    """
-    Sanitize the name by replacing invalid characters with '-'
-    """
-    name = name.lstrip()
-    if not name:
-        raise ValueError("Provided FASTA/FASTQ is empty or consists only of whitespace")
-    return re.sub(r'[\\/:?.,\'"<>| ]', "-", name)
-
-
-########################################################################
-# Extract basename
-########################################################################
-
-
-def extract_basename(fastq_path: str) -> str:
-    name = Path(fastq_path).name
-    name = re.sub(r"\..*$", "", name)  # Remove file extension
-    return _sanitize_name(name)
-
-
-########################################################################
-# Convert allele file to dictionary type fasta format
-########################################################################
-
-
-def dictionize_allele(path_fasta: str | Path) -> dict[str, str]:
-    return {_sanitize_name(name): seq.upper() for name, seq, _ in mappy.fastx_read(str(path_fasta))}
-
-
-########################################################################
-# Export fasta files as single-FASTA format
-########################################################################
-
-
-def export_fasta_files(TEMPDIR: Path, FASTA_ALLELES: dict, NAME: str) -> None:
-    """
-    This function exports FASTA files in single-FASTA format.
-
-    :param TEMPDIR: Temporary directory Path object where the output files will be saved.
-    :param FASTA_ALLELES: Dictionary containing identifier and sequence pairs.
-    :param NAME: Name to be included in the output path.
-    """
-    for identifier, sequence in FASTA_ALLELES.items():
-        contents = "\n".join([">" + identifier, sequence]) + "\n"
-        output_fasta = Path(TEMPDIR, NAME, "fasta", f"{identifier}.fasta")
-        output_fasta.write_text(contents)

DAJIN2-0.4.1/src/DAJIN2/utils/fastx_handler.py

@@ -1,42 +0,0 @@
-from __future__ import annotations
-
-import gzip
-from pathlib import Path
-
-#################################################
-# save_concatenated_fastx
-#################################################
-
-
-def extract_extention(file_path: Path) -> str:
-    suffixes = file_path.suffixes
-    return "".join(suffixes[-2:]) if len(suffixes) >= 2 else suffixes[0]
-
-
-def is_gzip_file(file_name: Path) -> bool:
-    """Check if a file is a GZip compressed file."""
-    try:
-        with file_name.open("rb") as f:
-            return f.read(2) == b"\x1f\x8b"
-    except IOError:
-        return False
-
-
-def save_fastq_as_gzip(TEMPDIR: Path, path_fastx: list[Path], barcode: str) -> None:
-    """Merge gzip and non-gzip files into a single gzip file."""
-    with gzip.open(Path(TEMPDIR, barcode, "fastq", f"{barcode}.fastq.gz"), "wb") as merged_file:
-        for file_name in path_fastx:
-            if is_gzip_file(file_name):
-                with gzip.open(file_name, "rb") as f:
-                    merged_file.write(f.read())
-            else:
-                with open(file_name, "r") as f:
-                    merged_file.write(f.read().encode())
-
-
-def save_concatenated_fastx(TEMPDIR: Path, directory: str) -> None:
-    fastx_suffix = {".fa", ".fq", ".fasta", ".fastq", ".fa.gz", ".fq.gz", ".fasta.gz", ".fastq.gz"}
-    path_directory = Path(directory)
-    barcode = path_directory.stem
-    path_fastx = [path for path in path_directory.iterdir() if extract_extention(path) in fastx_suffix]
-    save_fastq_as_gzip(TEMPDIR, path_fastx, barcode)