gtdb_tree

A library for parsing Newick format files, especially GTDB tree files.

Features

  • Parse Newick formatted strings into a structured representation of trees.
  • Handle various formats of Newick strings, including those with bootstrap values and distances.

Installation

Add this crate to your Cargo.toml:

[dependencies]
gtdb_tree = "0.1.9"

Usage

Here's a simple example of how to use the library:

use gtdb_tree::tree::parse_tree;

fn main() {
    let newick_str = "((A:0.1,B:0.2):0.3,C:0.4);";
    match parse_tree(newick_str) {
        Ok(nodes) => println!("Parsed nodes: {:?}", nodes),
        Err(e) => println!("Error parsing: {:?}", e),
    }
}

Python Usage

A Python package for parsing GTDB trees using Rust.

Installation

pip install gtdb_tree

import gtdb_tree

result = gtdb_tree.parse_tree("((A:0.1,B:0.2):0.3,C:0.4);")
print(result)

Advanced Usage

Custom Node Parser

You can provide a custom parser function to handle special node formats:

import gtdb_tree

def custom_parser(node_str):
    # Custom parsing logic
    name, length = node_str.split(':')
    return name, 100.0, float(length)  # name, bootstrap, length

result = gtdb_tree.parse_tree("((A:0.1,B:0.2):0.3,C:0.4);", custom_parser=custom_parser)
print(result)

Working with Node Objects

Each Node object in the result has the following attributes:

  • id: Unique identifier for the node
  • name: Name of the node
  • bootstrap: Bootstrap value (if available)
  • length: Branch length
  • parent: ID of the parent node

Project links

Data verified by PyPI on Sep 7, 2024
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for dagou from gravatar.com dagou

Credits

Author: dagou <eric9n@gmail.com>

GitHub Statistics

Data verified by PyPI on Sep 7, 2024
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License (MIT)

Requires

Python >=3.8

Tags

gtdb tree parser rust

Classifiers

Report project as malware

Metadata

Project links

Data verified by PyPI on Sep 7, 2024
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for dagou from gravatar.com dagou

Credits

Author: dagou <eric9n@gmail.com>

GitHub Statistics

Data verified by PyPI on Sep 7, 2024
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License (MIT)

Requires

Python >=3.8

Tags

gtdb tree parser rust

Classifiers

Report project as malware

Release files for gtdb-tree 0.1.9

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for gtdb-tree 0.1.9
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gtdb_tree-0.1.9.tar.gz 8.9 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for gtdb-tree 0.1.9
File
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gtdb_tree-0.1.9-pp310-pypy310_pp73-musllinux_1_2_armv7l.whl 543.1 kB PyPy 3.10 PyPy 3.10 7.3 Linux musl 1.2+ ARMv7l Details
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gtdb_tree-0.1.9-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl 313.2 kB CPython 3.10 CPython 3.10 Linux glibc 2.17+ PowerPC 64-le Details
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gtdb_tree-0.1.9-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.whl 289.2 kB CPython 3.10 CPython 3.10 Linux glibc 2.5+ x86-32 Details
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gtdb_tree-0.1.9-cp39-cp39-musllinux_1_2_i686.whl 464.2 kB CPython 3.9 CPython 3.9 Linux musl 1.2+ x86-32 Details
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gtdb_tree-0.1.9-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl 322.6 kB CPython 3.9 CPython 3.9 Linux glibc 2.17+ IBM System/390x Details
gtdb_tree-0.1.9-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl 313.9 kB CPython 3.9 CPython 3.9 Linux glibc 2.17+ PowerPC 64-le Details
gtdb_tree-0.1.9-cp39-cp39-manylinux_2_17_armv7l.manylinux2014_armv7l.whl 287.6 kB CPython 3.9 CPython 3.9 Linux glibc 2.17+ ARMv7l Details
gtdb_tree-0.1.9-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 282.5 kB CPython 3.9 CPython 3.9 Linux glibc 2.17+ ARM64 Details
gtdb_tree-0.1.9-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl 289.9 kB CPython 3.9 CPython 3.9 Linux glibc 2.5+ x86-32 Details
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gtdb_tree-0.1.9-cp38-cp38-musllinux_1_2_i686.whl 464.3 kB CPython 3.8 CPython 3.8 Linux musl 1.2+ x86-32 Details
gtdb_tree-0.1.9-cp38-cp38-musllinux_1_2_armv7l.whl 542.6 kB CPython 3.8 CPython 3.8 Linux musl 1.2+ ARMv7l Details
gtdb_tree-0.1.9-cp38-cp38-musllinux_1_2_aarch64.whl 460.0 kB CPython 3.8 CPython 3.8 Linux musl 1.2+ ARM64 Details
gtdb_tree-0.1.9-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 276.8 kB CPython 3.8 CPython 3.8 Linux glibc 2.17+ x86-64 Details
gtdb_tree-0.1.9-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl 322.5 kB CPython 3.8 CPython 3.8 Linux glibc 2.17+ IBM System/390x Details
gtdb_tree-0.1.9-cp38-cp38-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl 314.1 kB CPython 3.8 CPython 3.8 Linux glibc 2.17+ PowerPC 64-le Details
gtdb_tree-0.1.9-cp38-cp38-manylinux_2_17_armv7l.manylinux2014_armv7l.whl 287.5 kB CPython 3.8 CPython 3.8 Linux glibc 2.17+ ARMv7l Details
gtdb_tree-0.1.9-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 282.4 kB CPython 3.8 CPython 3.8 Linux glibc 2.17+ ARM64 Details
gtdb_tree-0.1.9-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl 289.3 kB CPython 3.8 CPython 3.8 Linux glibc 2.5+ x86-32 Details

Total release size: 31.8 MB

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Release files / gtdb_tree-0.1.9-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Release files / gtdb_tree-0.1.9-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl

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This release

0.1.9 This release

95 release files

0.1.8

95 release files

0.1.6

95 release files

0.1.5

2 release files

0.1.4

12 release files

0.1.2

4 release files

0.1.0

2 release files

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