virusdicer 0.1.1__tar.gz

virusdicer-0.1.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Dmitry Bespiatykh
+
+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.

virusdicer-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: virusdicer
+Version: 0.1.1
+Summary: CLI toolkit for building distance-based proteomic virus phylogenies from protein or nucleotide inputs
+Author: Dmitry Bespiatykh
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: pyrodigal-gv
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Dynamic: license-file
+
+<p align="center">
+  <img src="https://github.com/dbespiatykh/VirusDicer/blob/main/assets/logo.png?raw=true" alt="virusdicer logo" height=200>
+</p>
+<hr>
+
+`VirusDicer` is a command-line toolkit for building distance-based proteomic
+virus phylogenies from protein or nucleotide inputs.
+
+## Workflow
+
+<!-- workflow-mermaid:start -->
+<details>
+<summary>Show workflow chart</summary>
+
+```mermaid
+flowchart TD
+    input[Input sequences or table] --> mode{Input type}
+    mode -->|--in-fna| orfs[Predict ORFs with pyrodigal-gv]
+    mode -->|--in-faa| faa[Prepare protein FASTA]
+    mode -->|--in-dmnd-tab| dmnd[DIAMOND output table]
+    orfs --> faa
+    faa --> blast[DIAMOND makedb + blastp]
+    blast --> dmnd
+    dmnd --> filter[Filter DIAMOND hits]
+    filter --> best[Best hit per query protein and target genome]
+    best --> score[Symmetric genome bitscore matrix]
+    score --> dice[Dice distance matrix]
+    dice --> support{Support replicates?}
+    support -->|yes| reps[Bootstrap or jackknife replicates]
+    reps --> tree[BioNJ tree with midpoint rooting]
+    support -->|no| tree
+    tree --> final[Final Newick tree]
+```
+
+Dice distance:
+
+$$
+D_{AB} = 1 - \frac{2AB}{AA + BB}
+$$
+
+where `AB` is the symmetric bitscore between genomes `A` and `B`, and `AA`
+and `BB` are their self bitscores.
+</details>
+<!-- workflow-mermaid:end -->
+
+## Installation
+
+External dependencies:
+
+- [DIAMOND](https://github.com/bbuchfink/diamond) (tested with v2.1.24)
+- [R](https://cran.r-project.org/) (tested with v4.5.3)
+- R package [ape](https://cran.r-project.org/web/packages/ape/index.html) (tested with v5.8.1)
+
+### If you have all the external dependencies:
+
+```bash
+python3 -m venv venv
+source venv/bin/activate
+pip install virusdicer
+```
+
+### Conda:
+```bash
+conda env create --file https://raw.githubusercontent.com/dbespiatykh/VirusDicer/refs/heads/main/environment.yml
+conda activate virusdicer
+virusdicer -h
+```
+
+## Usage
+```
+Usage: virusdicer [OPTIONS]
+
+  `VirusDicer` builds a distance-based proteomic virus phylogeny.
+
+  Examples:
+    virusdicer --in-fna genomes/ -o virusdicer_out
+    virusdicer --in-dmnd-tab hits.tsv -o virusdicer_out
+
+  Provide either FAA/FNA inputs for a full end-to-end run, or a correctly
+  formatted all-vs-all DIAMOND outfmt6 table with self hits and columns:
+  qseqid sseqid pident length qlen slen evalue bitscore
+
+Options:
+  --in-faa TEXT                   Protein FAA inputs. Provide one or more files or directories. Provide one or more
+                                  values after the option name.  [default: all_proteins.faa]
+  --in-fna TEXT                   Nucleotide FASTA inputs used for ORF calling. Provide one or more files or
+                                  directories. Provide one or more values after the option name.
+  --in-dmnd-tab TEXT              Use an existing DIAMOND outfmt6 table instead of running DIAMOND.
+  -o, --output-dir TEXT           Write pipeline outputs to this directory.  [default: virusdicer_out]
+  -t, --threads INTEGER           Total worker budget for pyrodigal-gv ORF prediction, DIAMOND, and support
+                                  replicate computation.  [default: 4]
+  --diamond-sensitivity INTEGER   DIAMOND search sensitivity level.
+                                  
+                                  1 default
+                                  2 fast
+                                  3 mid-sensitive
+                                  4 sensitive
+                                  5 more-sensitive
+                                  6 very-sensitive (default)
+                                  7 ultra-sensitive
+  --min-pident FLOAT              Minimum percent identity retained from DIAMOND hits.  [default: 30.0]
+  --min-aalen FLOAT               Minimum alignment length in amino acids retained from DIAMOND hits.  [default:
+                                  30.0]
+  --max-evalue FLOAT              Maximum e-value retained from DIAMOND hits.  [default: 0.01]
+  --min-bitscore FLOAT            Minimum bitscore retained from DIAMOND hits.  [default: 30.0]
+  --min-qcov FLOAT                Minimum query coverage retained from DIAMOND hits. Accepts values like 50 or 0.5.
+                                  [default: 0.5]
+  --min-scov FLOAT                Minimum subject coverage retained from DIAMOND hits. Accepts values like 50 or
+                                  0.5.  [default: 0.5]
+  --min-protein-len INTEGER       Exclude hits where either protein is shorter than this.  [default: 50]
+  --id-regex TEXT                 Regex with one capture group used to derive genome IDs from protein IDs.  [default:
+                                  ^(.*)_\d+$]
+  --write-score-matrix            Write the symmetric genome-vs-genome bitscore matrix.
+  --support-mode [bootstrap|jackknife]
+                                  Resampling strategy used when --support-replicates is greater than zero.  [default:
+                                  bootstrap]
+  --support-replicates INTEGER    Number of protein-level support replicates to compute for branch support.  [default:
+                                  0]
+  --jackknife-fraction FLOAT      Fraction of proteins to keep per genome in each jackknife replicate.  [default: 0.5]
+  --support-seed INTEGER          Random seed for bootstrap or jackknife replicate generation.  [default: 1984]
+  -v, --version                   Show the version and exit.
+  -h, --help                      Show this message and exit.
+
+```
+
+From nucleotide FASTAs:
+
+```bash
+virusdicer --in-fna genomes/ -o virusdicer_out
+```
+
+From protein FASTAs:
+
+```bash
+virusdicer --in-faa faa/ -o virusdicer_out
+```
+
+From a DIAMOND output table:
+
+```bash
+diamond blastp \
+  --query faa \
+  --db db \
+  --out diamond_output.tsv \
+  --outfmt 6 qseqid sseqid pident length qlen slen evalue bitscore \
+  --max-target-seqs 0 \
+  --evalue 1000.0 \
+  --more-sensitive
+
+
+virusdicer --in-dmnd-tab diamond_output.tsv -o virusdicer_out
+```
+
+With bootstrap support:
+
+```bash
+virusdicer --in-fna genomes/ -o virusdicer_out \
+  --support-replicates 1000 \
+  --support-mode bootstrap
+```
+
+## Main output
+
+- `virusdicer_out/dice_distance.tsv` - Distance matrix
+- `virusdicer_out/genome_bitscore.tsv` when `--write-score-matrix` is used - Score matrix
+- `virusdicer_out/bionj.nwk` - BioNJ phylogeny
+
+
+## Citation
+
+- Buchfink, B., Reuter, K. & Drost, HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x
+
+- Emmanuel Paradis, Julien Claude, Korbinian Strimmer, APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, Volume 20, Issue 2, January 2004, Pages 289–290, https://doi.org/10.1093/bioinformatics/btg412
+
+- O Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data., Molecular Biology and Evolution, Volume 14, Issue 7, Jul 1997, Pages 685–695, https://doi.org/10.1093/oxfordjournals.molbev.a025808
+
+- R Core Team (2026). _R: A Language and Environment for Statistical Computing_. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
+
+- Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). https://doi.org/10.1186/1471-2105-11-119
+
+- Larralde, M., (2022). Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. Journal of Open Source Software, 7(72), 4296, https://doi.org/10.21105/joss.04296
+
+- Camargo, A.P., Roux, S., Schulz, F. et al. Identification of mobile genetic elements with geNomad. Nat Biotechnol 42, 1303–1312 (2024). https://doi.org/10.1038/s41587-023-01953-y

virusdicer-0.1.1/README.md

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+<p align="center">
+  <img src="https://github.com/dbespiatykh/VirusDicer/blob/main/assets/logo.png?raw=true" alt="virusdicer logo" height=200>
+</p>
+<hr>
+
+`VirusDicer` is a command-line toolkit for building distance-based proteomic
+virus phylogenies from protein or nucleotide inputs.
+
+## Workflow
+
+<!-- workflow-mermaid:start -->
+<details>
+<summary>Show workflow chart</summary>
+
+```mermaid
+flowchart TD
+    input[Input sequences or table] --> mode{Input type}
+    mode -->|--in-fna| orfs[Predict ORFs with pyrodigal-gv]
+    mode -->|--in-faa| faa[Prepare protein FASTA]
+    mode -->|--in-dmnd-tab| dmnd[DIAMOND output table]
+    orfs --> faa
+    faa --> blast[DIAMOND makedb + blastp]
+    blast --> dmnd
+    dmnd --> filter[Filter DIAMOND hits]
+    filter --> best[Best hit per query protein and target genome]
+    best --> score[Symmetric genome bitscore matrix]
+    score --> dice[Dice distance matrix]
+    dice --> support{Support replicates?}
+    support -->|yes| reps[Bootstrap or jackknife replicates]
+    reps --> tree[BioNJ tree with midpoint rooting]
+    support -->|no| tree
+    tree --> final[Final Newick tree]
+```
+
+Dice distance:
+
+$$
+D_{AB} = 1 - \frac{2AB}{AA + BB}
+$$
+
+where `AB` is the symmetric bitscore between genomes `A` and `B`, and `AA`
+and `BB` are their self bitscores.
+</details>
+<!-- workflow-mermaid:end -->
+
+## Installation
+
+External dependencies:
+
+- [DIAMOND](https://github.com/bbuchfink/diamond) (tested with v2.1.24)
+- [R](https://cran.r-project.org/) (tested with v4.5.3)
+- R package [ape](https://cran.r-project.org/web/packages/ape/index.html) (tested with v5.8.1)
+
+### If you have all the external dependencies:
+
+```bash
+python3 -m venv venv
+source venv/bin/activate
+pip install virusdicer
+```
+
+### Conda:
+```bash
+conda env create --file https://raw.githubusercontent.com/dbespiatykh/VirusDicer/refs/heads/main/environment.yml
+conda activate virusdicer
+virusdicer -h
+```
+
+## Usage
+```
+Usage: virusdicer [OPTIONS]
+
+  `VirusDicer` builds a distance-based proteomic virus phylogeny.
+
+  Examples:
+    virusdicer --in-fna genomes/ -o virusdicer_out
+    virusdicer --in-dmnd-tab hits.tsv -o virusdicer_out
+
+  Provide either FAA/FNA inputs for a full end-to-end run, or a correctly
+  formatted all-vs-all DIAMOND outfmt6 table with self hits and columns:
+  qseqid sseqid pident length qlen slen evalue bitscore
+
+Options:
+  --in-faa TEXT                   Protein FAA inputs. Provide one or more files or directories. Provide one or more
+                                  values after the option name.  [default: all_proteins.faa]
+  --in-fna TEXT                   Nucleotide FASTA inputs used for ORF calling. Provide one or more files or
+                                  directories. Provide one or more values after the option name.
+  --in-dmnd-tab TEXT              Use an existing DIAMOND outfmt6 table instead of running DIAMOND.
+  -o, --output-dir TEXT           Write pipeline outputs to this directory.  [default: virusdicer_out]
+  -t, --threads INTEGER           Total worker budget for pyrodigal-gv ORF prediction, DIAMOND, and support
+                                  replicate computation.  [default: 4]
+  --diamond-sensitivity INTEGER   DIAMOND search sensitivity level.
+                                  
+                                  1 default
+                                  2 fast
+                                  3 mid-sensitive
+                                  4 sensitive
+                                  5 more-sensitive
+                                  6 very-sensitive (default)
+                                  7 ultra-sensitive
+  --min-pident FLOAT              Minimum percent identity retained from DIAMOND hits.  [default: 30.0]
+  --min-aalen FLOAT               Minimum alignment length in amino acids retained from DIAMOND hits.  [default:
+                                  30.0]
+  --max-evalue FLOAT              Maximum e-value retained from DIAMOND hits.  [default: 0.01]
+  --min-bitscore FLOAT            Minimum bitscore retained from DIAMOND hits.  [default: 30.0]
+  --min-qcov FLOAT                Minimum query coverage retained from DIAMOND hits. Accepts values like 50 or 0.5.
+                                  [default: 0.5]
+  --min-scov FLOAT                Minimum subject coverage retained from DIAMOND hits. Accepts values like 50 or
+                                  0.5.  [default: 0.5]
+  --min-protein-len INTEGER       Exclude hits where either protein is shorter than this.  [default: 50]
+  --id-regex TEXT                 Regex with one capture group used to derive genome IDs from protein IDs.  [default:
+                                  ^(.*)_\d+$]
+  --write-score-matrix            Write the symmetric genome-vs-genome bitscore matrix.
+  --support-mode [bootstrap|jackknife]
+                                  Resampling strategy used when --support-replicates is greater than zero.  [default:
+                                  bootstrap]
+  --support-replicates INTEGER    Number of protein-level support replicates to compute for branch support.  [default:
+                                  0]
+  --jackknife-fraction FLOAT      Fraction of proteins to keep per genome in each jackknife replicate.  [default: 0.5]
+  --support-seed INTEGER          Random seed for bootstrap or jackknife replicate generation.  [default: 1984]
+  -v, --version                   Show the version and exit.
+  -h, --help                      Show this message and exit.
+
+```
+
+From nucleotide FASTAs:
+
+```bash
+virusdicer --in-fna genomes/ -o virusdicer_out
+```
+
+From protein FASTAs:
+
+```bash
+virusdicer --in-faa faa/ -o virusdicer_out
+```
+
+From a DIAMOND output table:
+
+```bash
+diamond blastp \
+  --query faa \
+  --db db \
+  --out diamond_output.tsv \
+  --outfmt 6 qseqid sseqid pident length qlen slen evalue bitscore \
+  --max-target-seqs 0 \
+  --evalue 1000.0 \
+  --more-sensitive
+
+
+virusdicer --in-dmnd-tab diamond_output.tsv -o virusdicer_out
+```
+
+With bootstrap support:
+
+```bash
+virusdicer --in-fna genomes/ -o virusdicer_out \
+  --support-replicates 1000 \
+  --support-mode bootstrap
+```
+
+## Main output
+
+- `virusdicer_out/dice_distance.tsv` - Distance matrix
+- `virusdicer_out/genome_bitscore.tsv` when `--write-score-matrix` is used - Score matrix
+- `virusdicer_out/bionj.nwk` - BioNJ phylogeny
+
+
+## Citation
+
+- Buchfink, B., Reuter, K. & Drost, HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x
+
+- Emmanuel Paradis, Julien Claude, Korbinian Strimmer, APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, Volume 20, Issue 2, January 2004, Pages 289–290, https://doi.org/10.1093/bioinformatics/btg412
+
+- O Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data., Molecular Biology and Evolution, Volume 14, Issue 7, Jul 1997, Pages 685–695, https://doi.org/10.1093/oxfordjournals.molbev.a025808
+
+- R Core Team (2026). _R: A Language and Environment for Statistical Computing_. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
+
+- Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). https://doi.org/10.1186/1471-2105-11-119
+
+- Larralde, M., (2022). Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. Journal of Open Source Software, 7(72), 4296, https://doi.org/10.21105/joss.04296
+
+- Camargo, A.P., Roux, S., Schulz, F. et al. Identification of mobile genetic elements with geNomad. Nat Biotechnol 42, 1303–1312 (2024). https://doi.org/10.1038/s41587-023-01953-y

virusdicer-0.1.1/pyproject.toml

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+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools>=61"]
+
+[project]
+name = "virusdicer"
+dynamic = ["version"]
+description = "CLI toolkit for building distance-based proteomic virus phylogenies from protein or nucleotide inputs"
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.10"
+authors = [
+    { name = "Dmitry Bespiatykh" },
+]
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "click",
+    "pyrodigal-gv",
+]
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "pytest",
+    "pytest-cov",
+]
+
+[project.scripts]
+virusdicer = "virusdicer.cli:main"
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+
+[tool.setuptools.dynamic]
+version = { attr = "virusdicer.__version__" }
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.black]
+line-length = 120
+target-version = ["py310"]
+extend-exclude = """
+(
+    /venv
+  | /__pycache__
+  | /codex_.*
+  | /virusdicer_out
+)
+"""
+
+[tool.pytest.ini_options]
+addopts = "--cov=virusdicer --cov-report=term-missing"
+testpaths = ["tests"]
+
+[tool.coverage.run]
+branch = true
+source = ["virusdicer"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = false

virusdicer-0.1.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

virusdicer-0.1.1/src/virusdicer/__init__.py

@@ -0,0 +1,5 @@
+"""
+`VirusDicer` is a CLI toolkit for building distance-based proteomic virus phylogenies from protein or nucleotide inputs.
+"""
+
+__version__ = "0.1.1"

virusdicer-0.1.1/src/virusdicer/__main__.py

@@ -0,0 +1,7 @@
+"""Module entry point for `python -m virusdicer`."""
+
+from virusdicer.cli import main
+
+
+if __name__ == "__main__":
+    main()