FracSim 1.0.0__tar.gz

fracsim-1.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Julian
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

fracsim-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: FracSim
+Version: 1.0.0
+Summary: a FracMinHash-based genome similarity estimator for bacteria
+Home-page: https://github.com/zhuyu534/FracSim.git
+Author: YuZhu
+Author-email: zhuyu1068@gmail.com
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mmh3>=4.0.0
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: pytest>=7.0.0
+Requires-Dist: pytest-cov>=4.0.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+## <img src="images/logo.png" width="40" height="40" style="border-radius: 50%; vertical-align: text-bottom; margin-right: 8px;"> FracSim:fast bacterial genome similarity estimation using FracMinHash sketching
+
+[![Latest Version](https://img.shields.io/github/v/release/zhuyu534/FracSim?color=red)](https://github.com/zhuyu534/FracSim/releases)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+[![Platform](https://img.shields.io/badge/platform-linux%20%7C%20macos%20%7C%20windows-lightgrey?color=orange)](https://github.com/zhuyu534/FracSim)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+</div>
+
+FracSim is a **fast** and **accurate** tool for estimating **bacterial** genome similarity, based on the **FracMinHash** genome sketching algorithm. It compresses large genomes into compact hash sets to rapidly compute **Jaccard similarity** and **ANI (Average Nucleotide Identity)** between genomes.
+
+Whether for **species identification**, **strain typing**, or **large-scale genome comparison**, FracSim significantly reduces memory usage and computation time while maintaining high accuracy.
+
+Documents: https://zhuyu534.github.io/FracSim
+
+## ✨ Features
+
+- **Fast**: Uses FracMinHash sketching to dramatically lower memory footprint and runtime.
+- **Accurate**: Provides Jaccard index and ANI (Average Nucleotide Identity) estimates.
+- **Flexible**: Supports FASTA/Q formats, configurable k‑mer size and sampling rate.
+- **Easy to use**: Clean command‑line interface with multi‑threading support.
+- **Open source**: MIT licensed – contributions and usage are welcome.
+
+## 📦 Installation
+
+### Requirements
+- Python 3.8 or higher
+- pip package manager
+
+### Install from source 
+
+```bash
+git clone https://github.com/zhuyu534/FracSim.git
+cd FracSim
+pip install -e .

fracsim-1.0.0/README.md

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+## <img src="images/logo.png" width="40" height="40" style="border-radius: 50%; vertical-align: text-bottom; margin-right: 8px;"> FracSim:fast bacterial genome similarity estimation using FracMinHash sketching
+
+[![Latest Version](https://img.shields.io/github/v/release/zhuyu534/FracSim?color=red)](https://github.com/zhuyu534/FracSim/releases)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+[![Platform](https://img.shields.io/badge/platform-linux%20%7C%20macos%20%7C%20windows-lightgrey?color=orange)](https://github.com/zhuyu534/FracSim)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+</div>
+
+FracSim is a **fast** and **accurate** tool for estimating **bacterial** genome similarity, based on the **FracMinHash** genome sketching algorithm. It compresses large genomes into compact hash sets to rapidly compute **Jaccard similarity** and **ANI (Average Nucleotide Identity)** between genomes.
+
+Whether for **species identification**, **strain typing**, or **large-scale genome comparison**, FracSim significantly reduces memory usage and computation time while maintaining high accuracy.
+
+Documents: https://zhuyu534.github.io/FracSim
+
+## ✨ Features
+
+- **Fast**: Uses FracMinHash sketching to dramatically lower memory footprint and runtime.
+- **Accurate**: Provides Jaccard index and ANI (Average Nucleotide Identity) estimates.
+- **Flexible**: Supports FASTA/Q formats, configurable k‑mer size and sampling rate.
+- **Easy to use**: Clean command‑line interface with multi‑threading support.
+- **Open source**: MIT licensed – contributions and usage are welcome.
+
+## 📦 Installation
+
+### Requirements
+- Python 3.8 or higher
+- pip package manager
+
+### Install from source 
+
+```bash
+git clone https://github.com/zhuyu534/FracSim.git
+cd FracSim
+pip install -e .

fracsim-1.0.0/fracsim/FracSim.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: FracSim
+Version: 1.0.0
+Summary: a FracMinHash-based genome similarity estimator for bacteria
+Home-page: https://github.com/zhuyu534/FracSim.git
+Author: YuZhu
+Author-email: zhuyu1068@gmail.com
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mmh3>=4.0.0
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: pytest>=7.0.0
+Requires-Dist: pytest-cov>=4.0.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+## <img src="images/logo.png" width="40" height="40" style="border-radius: 50%; vertical-align: text-bottom; margin-right: 8px;"> FracSim:fast bacterial genome similarity estimation using FracMinHash sketching
+
+[![Latest Version](https://img.shields.io/github/v/release/zhuyu534/FracSim?color=red)](https://github.com/zhuyu534/FracSim/releases)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+[![Platform](https://img.shields.io/badge/platform-linux%20%7C%20macos%20%7C%20windows-lightgrey?color=orange)](https://github.com/zhuyu534/FracSim)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+</div>
+
+FracSim is a **fast** and **accurate** tool for estimating **bacterial** genome similarity, based on the **FracMinHash** genome sketching algorithm. It compresses large genomes into compact hash sets to rapidly compute **Jaccard similarity** and **ANI (Average Nucleotide Identity)** between genomes.
+
+Whether for **species identification**, **strain typing**, or **large-scale genome comparison**, FracSim significantly reduces memory usage and computation time while maintaining high accuracy.
+
+Documents: https://zhuyu534.github.io/FracSim
+
+## ✨ Features
+
+- **Fast**: Uses FracMinHash sketching to dramatically lower memory footprint and runtime.
+- **Accurate**: Provides Jaccard index and ANI (Average Nucleotide Identity) estimates.
+- **Flexible**: Supports FASTA/Q formats, configurable k‑mer size and sampling rate.
+- **Easy to use**: Clean command‑line interface with multi‑threading support.
+- **Open source**: MIT licensed – contributions and usage are welcome.
+
+## 📦 Installation
+
+### Requirements
+- Python 3.8 or higher
+- pip package manager
+
+### Install from source 
+
+```bash
+git clone https://github.com/zhuyu534/FracSim.git
+cd FracSim
+pip install -e .

fracsim-1.0.0/fracsim/FracSim.egg-info/SOURCES.txt

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+LICENSE
+README.md
+setup.py
+fracsim/FracSim.egg-info/PKG-INFO
+fracsim/FracSim.egg-info/SOURCES.txt
+fracsim/FracSim.egg-info/dependency_links.txt
+fracsim/FracSim.egg-info/entry_points.txt
+fracsim/FracSim.egg-info/requires.txt
+fracsim/FracSim.egg-info/top_level.txt
+fracsim/input_layer/__init__.py
+fracsim/input_layer/cli.py
+fracsim/input_layer/file_reader.py
+fracsim/input_layer/parser/__init__.py
+fracsim/input_layer/parser/fasta_parser.py
+fracsim/input_layer/parser/fastq_parser.py
+fracsim/output_layer/__init__.py
+fracsim/output_layer/console.py
+fracsim/output_layer/file_writer.py
+fracsim/output_layer/formatter.py
+fracsim/process_layer/__init__.py
+fracsim/process_layer/ani.py
+fracsim/process_layer/jaccard.py
+fracsim/process_layer/kmer_sketch.py
+fracsim/process_layer/models.py
+fracsim/utils/__init__.py
+fracsim/utils/hash.py
+fracsim/utils/validator.py

fracsim-1.0.0/fracsim/FracSim.egg-info/dependency_links.txt

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+

fracsim-1.0.0/fracsim/FracSim.egg-info/entry_points.txt

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+[console_scripts]
+fracsim = fracsim.main:main

fracsim-1.0.0/fracsim/FracSim.egg-info/requires.txt

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+mmh3>=4.0.0
+numpy>=1.21.0
+pytest>=7.0.0
+pytest-cov>=4.0.0

fracsim-1.0.0/fracsim/FracSim.egg-info/top_level.txt

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+input_layer
+output_layer
+process_layer
+utils

fracsim-1.0.0/fracsim/input_layer/__init__.py

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+"""输入层模块"""
+
+from .cli import parse_arguments
+from .file_reader import FileReader
+from .parser.fasta_parser import FastaParser
+from .parser.fastq_parser import FastqParser
+
+__all__ = [
+    'parse_arguments',
+    'FileReader',
+    'FastaParser',
+    'FastqParser'
+]

fracsim-1.0.0/fracsim/input_layer/cli.py

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+"""命令行参数解析模块"""
+
+import argparse  #命令行解析工具
+from ..version import __version__, __description__
+
+
+def parse_arguments():
+    """
+    解析命令行参数
+
+    Returns:
+        argparse.Namespace: 解析后的参数对象
+    """
+    parser = argparse.ArgumentParser(
+        usage="%(prog)s [-h] (-i INPUT [INPUT ...] | -l LIST) [options]",
+        description=__description__,
+        formatter_class=argparse.RawDescriptionHelpFormatter,  #控制帮助信息的格式
+        epilog="""
+Examples:
+  %(prog)s -i genome1.fasta genome2.fasta -k 21 -s 0.01 
+  %(prog)s -l genomes.txt -k 21 -s 0.001 -o output_dir/results.csv
+  %(prog)s -i genome1.fastq.gz genome2.fastq.gz --threads 4 --ani -V
+        """
+    )
+    
+    # 数据输入方式参数
+    input_group = parser.add_mutually_exclusive_group(required=True)  #创建互斥参数组，必须从该组中选择一个参数使用
+    input_group.add_argument(
+        '-i', '--input',
+        nargs='+',  #可接收多个值
+        help='从基因组文件输入，多个文件之间使用空格分隔'
+    )
+    input_group.add_argument(
+        '-l', '--list',
+        help='从包含基因组文件路径的列表文件输入（每行一个文件路径）'
+    )
+    
+
+    # 核心算法参数（K值、采样率、随机数种子）
+    parser.add_argument(
+        '-k', '--kmer-size',
+        type=int,
+        default=31,
+        help='k-mer长度，取值范围[1-64]，默认值31'
+    )
+    parser.add_argument(
+        '-s', '--scaled',
+        type=float,
+        default=0.01,
+        help='FracMinHash采样率，取值范围(0,1]，默认值0.01'
+    )
+    parser.add_argument(
+        '--seed',
+        type=int,
+        default=42,
+        help='哈希函数随机种子，默认值42'
+    )
+    
+
+# 计算选项
+    parser.add_argument(
+        '-a','--ani',
+        action='store_true',
+        help='计算输出ANI值（默认只计算Jaccard指数）'
+    )
+    parser.add_argument(
+        '-t','--threads',
+        type=int,
+        default=1,
+        help='计算线程数，默认值1'
+    )
+    parser.add_argument(
+        '-m','--min-similarity',
+        type=float,
+        default=0.00,
+        help='最小相似度阈值，只输出大于该值的结果，默认0.0'
+    )
+
+
+    # 输出选项参数
+    parser.add_argument(
+        '-o', '--output',
+        help='输出文件路径'
+    )
+    parser.add_argument(
+        '-f','--format',
+        choices=['table', 'json', 'csv'],
+        default='table',
+        help='结果输出格式，默认表格格式'
+    )
+    
+    
+    # 版本信息，输出过程信息
+    parser.add_argument(
+        '-v','--version',
+        action='version',
+        version=f'%(prog)s {__version__}',
+        help='版本信息'
+    )
+    parser.add_argument(
+        '-V','--verbose',
+        action='store_true',
+        help='输出详细信息'
+    )
+    
+    # 解析参数
+    args = parser.parse_args()
+    
+    # 参数验证
+    if args.kmer_size < 1 or args.kmer_size > 64:
+        parser.error("k-mer长度必须在1-64之间")
+    
+    if args.scaled <= 0 or args.scaled > 1:
+        parser.error("采样率必须在(0,1]范围内")
+    
+    if args.min_similarity < 0 or args.min_similarity > 1:
+        parser.error("最小相似度必须在0-1之间")
+    
+    return args

fracsim-1.0.0/fracsim/input_layer/file_reader.py

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+"""文件读取器模块"""
+
+import os   # 文件路径和存在性检查
+import sys  # 错误输出信息
+import gzip
+import bz2
+import lzma
+import zipfile
+import io
+from typing import List, Generator, Optional,Tuple   # 类型提示
+from .parser.fasta_parser import FastaParser   # 导入两个解析器
+from .parser.fastq_parser import FastqParser
+from ..process_layer.models import GenomeData  # 导入 GenomeData 类
+
+class FileReader:
+    """文件读取器类(支持压缩格式)"""
+    
+    def __init__(self, verbose=False):
+        """
+        初始化文件读取器
+        
+        Args:
+            verbose: 是否输出详细信息
+        """
+        self.verbose = verbose
+        self.fasta_parser = FastaParser()
+        self.fastq_parser = FastqParser()
+    
+    def get_file_list(self, input_files: List[str], list_file: Optional[str] = None) -> List[str]:
+        """
+        获取所有需要处理的文件列表
+        
+        Args:
+            input_files: 直接输入的文件
+            list_file: 包含文件路径的列表文件
+            
+        Returns:
+            List[str]: 文件路径列表
+        """
+        file_list = []
+        
+        if input_files:
+            file_list.extend(input_files)
+        
+        if list_file:
+            try:
+                with open(list_file, 'r') as f:
+                    for line in f:
+                        line = line.strip()
+                        if line and not line.startswith('#'):
+                            file_list.append(line)
+            except Exception as e:
+                sys.stderr.write(f"读取列表文件失败 {list_file}: {e}\n")
+                sys.exit(1)
+        
+        # 验证文件存在性
+        valid_files = []
+        for file_path in file_list:
+            if os.path.exists(file_path):
+                valid_files.append(file_path)
+            else:
+                sys.stderr.write(f"警告: 文件不存在 {file_path}\n")
+        
+        if not valid_files:
+            sys.stderr.write("错误: 没有有效的输入文件\n")
+            sys.exit(1)
+        
+        if self.verbose:
+            sys.stderr.write(f"找到 {len(valid_files)} 个有效文件\n")
+        
+        return valid_files
+    
+
+    # --------检测压缩类型---------
+    def _detect_compression(self, file_path: str) -> Tuple[Optional[str], str]:
+        """
+        检测文件是否为压缩格式，并返回 (压缩类型, 实际扩展名)
+        压缩类型: None, 'gz', 'bz2', 'xz', 'zip'
+        """
+        COMPRESS_EXTS = {'.gz': 'gz', '.bz2': 'bz2', '.xz': 'xz', '.zip': 'zip'}
+        ext = os.path.splitext(file_path)[1].lower()
+        if ext in COMPRESS_EXTS:
+            compression = COMPRESS_EXTS[ext]
+            # 去掉压缩后缀，再取一次扩展名作为实际格式
+            base_path = file_path[: -len(ext)]
+            base_ext = os.path.splitext(base_path)[1].lower()
+        else:
+            compression = None
+            base_ext = ext
+        return compression, base_ext
+
+    # ----------解压到内存----------
+    def _decompress_to_memory(self, file_path: str, compression: str) -> io.TextIOBase:
+        """
+        将压缩文件解压到内存，返回一个文本文件对象
+        支持 gz, bz2, xz, zip
+        """
+        mem_buffer = io.BytesIO()
+
+        try:
+            if compression == 'gz':
+                with gzip.open(file_path, 'rb') as src:
+                    while chunk := src.read(8192):
+                        mem_buffer.write(chunk)
+            elif compression == 'bz2':
+                with bz2.open(file_path, 'rb') as src:
+                    while chunk := src.read(8192):
+                        mem_buffer.write(chunk)
+            elif compression == 'xz':
+                with lzma.open(file_path, 'rb') as src:
+                    while chunk := src.read(8192):
+                        mem_buffer.write(chunk)
+            elif compression == 'zip':
+                with zipfile.ZipFile(file_path, 'r') as zipf:
+                    # 取第一个非目录文件
+                    for name in zipf.namelist():
+                        if not name.endswith('/'):
+                            with zipf.open(name, 'r') as src:
+                                while chunk := src.read(8192):
+                                    mem_buffer.write(chunk)
+                            break
+                    else:
+                        raise ValueError(f"ZIP文件中没有可读取的文件: {file_path}")
+            else:
+                raise ValueError(f"不支持的压缩格式: {compression}")
+        except Exception as e:
+            raise IOError(f"解压文件失败 {file_path}: {e}")
+
+        mem_buffer.seek(0)
+        # 将二进制流包装为文本流（解析器需要文本模式）
+        text_stream = io.TextIOWrapper(mem_buffer, encoding='utf-8')
+        # 保留 buffer 引用，防止被垃圾回收
+        text_stream._buffer = mem_buffer
+        return text_stream
+
+    
+    def read_sequences(self, file_path: str) -> Generator[tuple, None, None]:  # 序列读取接口，根据文件类型分配解析器
+        """
+        读取文件中的序列，支持普通文件及压缩格式（.gz/.bz2/.xz/.zip）
+        压缩文件将解压到内存后由解析器处理
+
+        Yields:
+            tuple: (序列ID, 序列字符串, 质量分数)
+        """
+        compression, base_ext = self._detect_compression(file_path)
+
+        try:
+            # 根据实际格式分发
+            if base_ext in ['.fasta', '.fa', '.fna', '.ffn', '.frn']:
+                if compression:
+                    # 压缩文件：解压到内存再解析
+                    mem_file = self._decompress_to_memory(file_path, compression)
+                    yield from self.fasta_parser.parse(mem_file)
+                else:
+                    yield from self.fasta_parser.parse(file_path)
+
+            elif base_ext in ['.fastq', '.fq']:
+                if compression:
+                    mem_file = self._decompress_to_memory(file_path, compression)
+                    yield from self.fastq_parser.parse(mem_file)
+                else:
+                    yield from self.fastq_parser.parse(file_path)
+
+            else:
+                # 未知扩展名，尝试自动检测（可能为压缩文件）
+                yield from self._auto_detect_parser(file_path, compression)
+
+        except Exception as e:
+            sys.stderr.write(f"读取文件失败 {file_path}: {e}\n")
+
+    #----------自动检测格式 ----------
+    def _auto_detect_parser(self, file_path: str, compression: Optional[str] = None) -> Generator[tuple, None, None]:
+        """
+        自动检测文件格式并解析（支持压缩文件）
+        """
+        try:
+            # 如果是压缩文件，先解压到内存
+            if compression:
+                mem_file = self._decompress_to_memory(file_path, compression)
+                # 递归调用自身，此时 compression=None，mem_file 作为文件对象
+                yield from self._auto_detect_parser(mem_file, compression=None)
+                return
+
+            # 此时 file_path 可能是普通路径或内存文件对象
+            if isinstance(file_path, io.TextIOBase):
+                f = file_path
+                need_rewind = True
+            else:
+                f = open(file_path, 'r')
+                need_rewind = False
+
+            with f:
+                # 读取第一个非空字符
+                first_char = None
+                for line in f:
+                    line = line.strip()
+                    if line:
+                        first_char = line[0]
+                        break
+                if not first_char:
+                    raise ValueError("文件为空")
+
+                f.seek(0)  # 重置指针
+
+                if first_char == '>':
+                    if isinstance(file_path, io.TextIOBase):
+                        yield from self.fasta_parser.parse(f)
+                    else:
+                        yield from self.fasta_parser.parse(file_path)
+                elif first_char == '@':
+                    if isinstance(file_path, io.TextIOBase):
+                        yield from self.fastq_parser.parse(f)
+                    else:
+                        yield from self.fastq_parser.parse(file_path)
+                else:
+                    raise ValueError(f"无法识别的文件格式，首字符: '{first_char}'")
+
+        except Exception as e:
+            raise ValueError(f"自动检测失败: {e}")
+        
+    def read_genome(self, file_path: str) -> GenomeData:
+        """
+        读取一个基因组文件的所有序列，返回包含多条序列的 GenomeData 对象
+    
+        Args:
+            file_path: 文件路径
+        
+        Returns:
+            GenomeData: 包含所有序列的基因组数据
+        """
+        sequences = []
+        genome_id = os.path.basename(file_path)  # 使用文件名作为基因组ID
+    
+        # 读取所有序列
+        for _, sequence, _ in self.read_sequences(file_path):
+            sequences.append(sequence)
+    
+        return GenomeData(
+            file_path=file_path,
+            seq_id=genome_id,
+            sequences=sequences  
+        )
+

fracsim-1.0.0/fracsim/input_layer/parser/__init__.py

@@ -0,0 +1,6 @@
+"""解析器模块"""
+
+from .fasta_parser import FastaParser
+from .fastq_parser import FastqParser
+
+__all__ = ['FastaParser', 'FastqParser']