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@Phlya Phlya released this 26 Oct 13:51
· 52 commits to master since this release
v1.0.0
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Learn about vigilant mode.

This is a major release with a lot of changes. The main ones are included below, but probably there are a lot of smaller ones too.

API changes

  • New HDF5-based storage format, with functions to write and read the files in coolpuppy.lib.io

  • New “user-facing” pileup function in python API for convenient single-step pileups, and with interface similar to cooltools.pileup

  • Pileups can be restricted using a genomic view (--view in CLI and view_df in API) in line with cooltools/bioframe (note that the expected has to be calculated for the same view, if used)

  • If using expected, by default each snippet is now normalized to expected and only averaged afterwards; this is controlled by ooe argument in API and --not-ooe argument in CLI)

  • Added options to split snippets based on strands, genomic distance, or both

  • Added option flip_negative_strand (API) and --flip-negative-strand (CLI) to flip features located on the negative strand

  • Added option to groupby snippets by their properties and generate multiple pileups in one run (groupby in API and --groupby in CLI)

  • Added option trans=True (API) and --trans (CLI) to generate inter-chromosomal (trans) pileups

  • Added option store_stripes=True (API) and --store_stripes (CLI) to store individual vertical and horizontal stripe pairs

  • Added advanced option (modify_2Dintervals_func of PileUpper.pileupsWithControls) to apply an arbitrary function to pairs of intervals before they are used for generating pileups (i.e. bedpe-style intervals generated internally from either bedpe- or bed-style input features)

  • Added advanced option to apply an arbitrary function to each snippet before averaging in API (postprocess_func of PileUpper.pileupsWithControls)

  • Added function divide_pups() (API) and dividepups.py (CLI) to divide two pileups

  • CLI detects headers of bed and bedpe files

  • Overall API and CLI argument names are aligned with cooltools wherever possible

Plotting changes

  • Changed names of plotpup.make_heatmap_grid() to plotpup.plot()
  • Added option plotpup.plot_stripes() (API) and --stripe (CLI) for plotting stripes
  • Added option --divide_pups (CLI) to plot the ratio of two pileups

Documentation

  • Extensive tutorials for both python API and CLI

Maintenance

  • Code restructured, so all CLI tools are in one package, and created .lib with shared internal functions in lib/io.py, lib/numutils.py, lib/puputils.py and lib/util.py

  • Tests migrated to github actions, and also running nbsmoke on the CLI notebook to ensure it runs without errors

  • Only support python >=3.8, cooltools >=0.5.2

Miscellaneous

  • Logging has been fixed so the --logLevel properly works
  • Removed the launch_pileups.sh script
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