tview 0.1.dev4__tar.gz

tview-0.1.dev4/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.14"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install package with dev dependencies
+        run: pip install ".[dev]"
+
+      - name: Run tests
+        run: pytest -v

tview-0.1.dev4/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    branches: [main]
+    tags:
+      - 'v*'
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  id-token: write  # Required for trusted publishing
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: [build]
+    runs-on: ubuntu-latest
+    if: always() && needs.build.result == 'success'
+    environment:
+      name: pypi
+      url: https://pypi.org/p/tview
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

tview-0.1.dev4/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

tview-0.1.dev4/LICENSE

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+MIT License
+
+Copyright (c) 2026 Troy Sincomb
+
+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.

tview-0.1.dev4/PKG-INFO

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+Metadata-Version: 2.4
+Name: tview
+Version: 0.1.dev4
+Summary: Publication-quality alignment viewer for nucleotide and amino acid sequences
+Author-email: Troy Sincomb <troysincomb@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/MurrellGroup/tview
+Project-URL: Repository, https://github.com/MurrellGroup/tview
+Project-URL: Issues, https://github.com/MurrellGroup/tview/issues
+Keywords: bioinformatics,alignment,samtools,tview,visualization,BAM,FASTA
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+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: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: click>=8.0
+Requires-Dist: pysam>=0.20; sys_platform != "win32"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: hypothesis>=6.0; extra == "dev"
+Dynamic: license-file
+
+# tview
+
+Publication-quality alignment viewer for nucleotide and amino acid sequences. A lightweight alternative to `samtools tview` that produces clean, stable image output.
+
+Supports **BAM files** (with reference FASTA), **pre-aligned FASTA** (e.g. MAFFT output), and **stacking** multiple inputs into a single figure.
+
+![BAM with indels](examples/indel_alignment.png)
+*BAM mode — SNP (yellow), 3bp deletion, 2bp insertion (purple columns), reverse-strand insertion*
+
+![FASTA amino acid alignment](examples/fasta_env_1-120.png)
+*FASTA mode — HIV Env protein alignment (HxB2 reference), amino acid palette*
+
+![Stacked BAMs](examples/stacked_bam.png)
+*Stacked mode — two BAM files sharing a reference and region*
+
+---
+
+## Installation
+
+```bash
+pip install tview
+```
+
+Installs `matplotlib`, `click`, and `pysam`.
+
+---
+
+## Quick Start
+
+### BAM file
+
+```bash
+tview \
+  --bam aligned.bam \
+  --ref reference.fa \
+  --region chr1:100-200 \
+  -o alignment.png
+```
+
+### Aligned FASTA (e.g. MAFFT output)
+
+The first sequence in the file is treated as the reference.
+
+```bash
+tview \
+  --fasta env_protein_aligned.fasta \
+  --palette aa \
+  -o env_alignment.png
+```
+
+### Subset columns from a FASTA alignment
+
+Use `--columns` with 1-based inclusive range to window into long alignments.
+
+```bash
+tview \
+  --fasta aligned.fasta \
+  --columns 1-120 \
+  --palette aa \
+  -o first_120_cols.png
+```
+
+---
+
+## Stacking Multiple Panels
+
+Each input file becomes a vertically stacked panel separated by a thin line. Panels are labeled on the left with the filename stem.
+
+### Multiple BAMs (shared reference and region)
+
+```bash
+tview \
+  --bam sample1.bam --bam sample2.bam --bam sample3.bam \
+  --ref reference.fa \
+  --region chr1:100-200 \
+  -o stacked.png
+```
+
+### Multiple FASTAs
+
+```bash
+tview \
+  --fasta group1_aligned.fasta --fasta group2_aligned.fasta \
+  --palette aa \
+  --columns 1-120 \
+  -o comparison.png
+```
+
+### Mix BAM and FASTA panels
+
+`--ref` and `--region` apply only to BAM panels; `--columns` applies only to FASTA panels.
+
+```bash
+tview \
+  --bam reads.bam \
+  --ref reference.fa \
+  --region chr1:100-200 \
+  --fasta protein_aligned.fasta \
+  --columns 1-120 \
+  -o mixed.png
+```
+
+BAM panels are rendered first (top), FASTA panels below.
+
+---
+
+## Piping from stdin
+
+Pass `-` to read file paths from stdin (one per line). Each path becomes its own panel.
+
+```bash
+# find → stacked panels
+find ./alignments -name "*.fasta" -type f | \
+  tview --fasta - --palette aa --columns 1-120 -o all.png
+
+# ls with pattern
+ls samples/*.bam | \
+  tview --bam - --ref ref.fa --region chr1:100-200 -o all_samples.png
+
+# single file via echo
+echo "my_alignment.fasta" | \
+  tview --fasta - --palette aa -o out.png
+```
+
+---
+
+## Python API
+
+The core functions are available as a Python library:
+
+```python
+from tview import fasta_panel, bam_panel, render_panels
+
+# FASTA alignment
+panel = fasta_panel("aligned.fasta", col_start=1, col_end=120)
+render_panels([panel], "output.png", palette="aa")
+
+# BAM alignment
+panel = bam_panel("sample.bam", "reference.fa", "chr1:100-200")
+render_panels([panel], "output.png")
+
+# Stack multiple panels
+panels = [
+    bam_panel("sample1.bam", "ref.fa", "chr1:100-200"),
+    bam_panel("sample2.bam", "ref.fa", "chr1:100-200"),
+]
+render_panels(panels, "stacked.png", dpi=300, fontsize=7, cell=0.14)
+```
+
+---
+
+## Visual Conventions
+
+| Element | Symbol | Style |
+|---------|--------|-------|
+| Match (forward) | `.` | light grey |
+| Match (reverse) | `,` | light grey, reduced opacity |
+| Mismatch | `A` `T` etc. | colored, yellow highlight, bold |
+| Mismatch (reverse) | `a` `t` etc. | lowercase, colored, yellow highlight |
+| Deletion | `-` | grey dash |
+| Insertion | colored bases | purple column shading |
+| Gap (ref in insertion col) | `-` | grey dash |
+| Gap (FASTA alignment) | `-` | grey dash |
+
+---
+
+## Color Palettes
+
+### `--palette nt` (default) — Nucleotides
+
+| Base | Color |
+|------|-------|
+| A | green `#4CAF50` |
+| C | blue `#2196F3` |
+| G | orange `#FF9800` |
+| T | red `#F44336` |
+
+### `--palette aa` — Amino Acids (Clustal-inspired)
+
+| Group | Residues | Color |
+|-------|----------|-------|
+| Hydrophobic | A V L I M F W P | blue `#2196F3` |
+| Positive charge | K R H | red `#F44336` |
+| Negative charge | D E | magenta `#E040FB` |
+| Polar uncharged | S T N Q | green `#4CAF50` |
+| Special | G C Y | orange `#FF9800` |
+
+---
+
+## Full Argument Reference
+
+```
+Usage: tview [OPTIONS]
+
+  Publication-quality alignment viewer (BAM or FASTA).
+
+Options:
+  --bam TEXT              BAM file(s) — each becomes a panel. Use '-' for stdin.
+  --ref PATH              Reference FASTA (required for BAM mode).
+  --region TEXT            Genomic region chr:start-end (required for BAM mode).
+  --fasta TEXT             Aligned FASTA file(s) — each becomes a panel. Use '-' for stdin.
+  --columns TEXT           Column range for FASTA, 1-based inclusive (e.g. 1-120).
+  -o, --output TEXT        Output image path.  [default: alignment.png]
+  --palette [nt|aa]        Color palette.  [default: nt]
+  --dpi INTEGER            Image resolution.  [default: 300]
+  --fontsize INTEGER       Base font size in points.  [default: 7]
+  --cell FLOAT             Cell size in inches.  [default: 0.14]
+  -h, --help               Show this message and exit.
+```
+
+| Argument | Description | Default |
+|----------|-------------|---------|
+| `--bam` | BAM file(s), each becomes a panel. Use `-` for stdin. | — |
+| `--ref` | Reference FASTA (required for BAM mode) | — |
+| `--region` | Genomic region `chr:start-end` (required for BAM) | — |
+| `--fasta` | Aligned FASTA file(s), each becomes a panel. Use `-` for stdin. | — |
+| `--columns` | Column range for FASTA, 1-based inclusive (e.g. `1-120`) | full alignment |
+| `-o, --output` | Output image path | `alignment.png` |
+| `--palette` | Color palette: `nt` or `aa` | `nt` |
+| `--dpi` | Image resolution | `300` |
+| `--fontsize` | Base font size in points | `7` |
+| `--cell` | Cell size in inches (controls spacing) | `0.14` |
+
+---
+
+## Tips for Publication Figures
+
+- Use `--dpi 300` (default) for print, `--dpi 150` for drafts.
+- Use `--cell 0.10` for denser layouts with many sequences, `--cell 0.18` for fewer.
+- Use `--fontsize 5` or `6` when displaying wide alignments (>100 columns).
+- The output format is determined by the file extension: `.png`, `.pdf`, `.svg` all work.
+- For Nature-style figures, `.pdf` or `.svg` output preserves vector text.
+
+```bash
+# Vector output for publication
+tview \
+  --fasta aligned.fasta \
+  --palette aa \
+  --columns 1-120 \
+  --cell 0.12 \
+  --fontsize 6 \
+  -o figure_2a.pdf
+```
+
+---
+
+## FASTA Input Format
+
+The FASTA input must be **pre-aligned** (e.g. by MAFFT, MUSCLE, Clustal). The first sequence is used as the reference for comparison. Gap characters (`-`) in the alignment are preserved and rendered as grey dashes.
+
+```
+>HxB2_reference
+MRVK---EKYQHLWRWGWRWGTMLLGMLMICS...
+>sample_001
+MRVKGIRKNAQHL----WRGGTLLLGMLMICS...
+>sample_002
+--------------------------MLMICS...
+```
+
+The x-axis labels count non-gap positions in the reference sequence (1, 10, 20, ...), so position numbers always correspond to the reference residue numbering regardless of gap columns.