Skip to content

Releases: guangzhaocs/segSHAPE

Release list

segSHAPE v0.1.1

segSHAPE v0.1.1 Latest
Latest

Choose a tag to compare

View all tags
@guangzhaocs guangzhaocs released this 19 Jun 13:57
v0.1.1
2eef781

segSHAPE v0.1.1

Bug-fix and documentation release. Fixes a broken clean install in v0.1.0 and slims the dependency set. No API or behavior changes.

Fixes

  • Declare missing runtime dependencies scikit-learn and pyarrow. v0.1.0 imported them but never declared them, so a fresh pip install segshape was broken — even segshape --version failed with ModuleNotFoundError: No module named 'sklearn', and segshape segment failed on pyarrow.
  • Remove the unused io/signal_reader.py module; drop the ont-fast5-api and h5py dependencies. signal_reader.py was an orphan never imported anywhere — the pipeline reads pod5 signal directly via pod5.Reader. This also removes an import failure on modern setuptools (≥81 dropped pkg_resources, which ont-fast5-api still imports).

Documentation

  • Add a PyPI downloads badge and reorder the badge row.
  • Make README doc/LICENSE links absolute so they render on the PyPI project page.
  • Document the tested ViennaRNA version (2.7.0).

Verified

In a fresh, isolated Python 3.10 environment installed from a clean build: all submodules import cleanly, the full test suite (115 tests) passes, and pip install pulls only the declared dependencies.

Install / upgrade

pip install -U segshape

Full changelog: v0.1.0...v0.1.1

Assets 2
Loading

segSHAPE v0.1.0

segSHAPE v0.1.0

Choose a tag to compare

View all tags
@guangzhaocs guangzhaocs released this 19 Jun 11:14
v0.1.0
c62dc8c

segSHAPE v0.1.0 — first public release

End-to-end pipeline that turns raw Oxford Nanopore direct-RNA signal into a SHAPE-constrained RNA secondary structure. Supports both RNA002 and RNA004 chemistries.

Highlights

  • Full 7-step pipeline: pod5index → dorado-extract → segment → event-align → mod-calling → fold, plus evaluate and plot.
  • Find-peaks signal segmentation + anchored Viterbi event alignment.
  • Per-position modification / reactivity calling (treated vs. control), folded with ViennaRNA RNAfold.
  • Bundled ONT k-mer tables and RNAfold parameter file — nothing extra to download.

Install

​ conda create -n segshape python=3.10 && conda activate segshape ​

​ pip install segshape ​

​ conda install -c bioconda viennarna # RNAfold for the folding step ​

Links

Loading