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Change Log

All notable changes to Rp-Bp will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased] - started 2024-03

[3.0.4] 2024-03-14

Fixed

  • Pandas str.split API in summarize_rpbp_predictions.py

[3.0.3] 2023-09-13

Changed

  • Requires pbiotools >= 4.0.2

[3.0.2] 2023-05-19

Added

  • riboseq_sample_name_map, riboseq_condition_name_map to rpbp_predictions_dashboard.py
  • Exception for duplicated transcript ids with de novo annotation.

Fixed

  • STAR output
  • Redundant transcripts with de novo annotation in summarize_rpbp_predictions.py
  • ORF numbers in labels

[3.0.1] 2023-02-10

Changed

  • I/O: ensure bool in config, remove symlinks
  • Documentation

Fixed

  • Missing GTF attributes

Added

  • Dash assets to MANIFEST

[3.0.0] 2023-02-06

Changed

  • Upgrade all dependencies/required packages, install via bioconda
  • Location of (compiled) Stan models
  • PyStan 2 to CmdStanPy API
  • Handling of ORF labels
  • Documentation

Removed

  • PyStan dependency
  • Fitted parameters from output _location and _scale
  • orf_type filtering for translation prediction
  • GFF3 support
  • Unfiltered predictions, unless [--write-unfiltered] is set
  • QTI-seq, various plotting/reporting scripts, notebooks

Fixed

  • Stan models transformed data/parameters name/definition (no-periodicity.stan, gaussian-naive-bayes.stan)
  • CmdStanPy logging

Added

  • Regression tests, pre-commit, GitHub CI workflow, etc.
  • Options handling for prepare_rpbp_genome
  • Retrieve gene_id, etc. from annotations
  • Dashboad applications to replace PDF reports
  • Data wrangling: summarize_rpbp_profile_construction.py, and summarize_rpbp_predictions.py
  • ribo_utils
  • orf_profile_construction scripts from pbiotools.ribo

[2.0.0] 2019-05-24

Changed

  • Configure setup() using setup.cfg, add pbio, update install via requirements.

Added

  • Config file for RTD
  • Module with all defaults parameters, handling options for external dependencies
  • Add option to force the pickling of the Stan models during installation ISSUE #88.

Fixed

  • Build RTD documentation (add autodoc_mock_imports, empty docs/requirements.txt)
  • Missing parameters in function calls, hard coded defaults
  • YAMLLoadWarning
  • Fall back to multiprocessing in estimate_orf_bayes_factors, and extract_orf_profiles
  • Stan assignment operator in models
  • ORF labels in prepare_rpbp_genome, label_orfs and extract_orf_coordinates, see ISSUE #96.

Removed

  • Transcript exons file (unused)

[1.1.12] - 2018-03-14

Changed

  • Example dataset updated and moved to new address. Updated documentation.
  • predict_translated_orfs and select_final_prediction_set modified such that Rp-chi pipeline is used only if chi_square_only is in config file, otherwise Rp-Bp is used.
  • Handling of options passed to flexbar via arguments to run_all_rpbp_instances, run_rpbp_pipeline, create_orf_profiles and create_base_genome_profile.
  • Handling of additional options passed to star via arguments, mainly to create_base_genome_profile.

Removed

  • Removed config option seqids_to_keep for compatibility with extract_metagene_profiles that does not use this option anymore. This has also been removed from the example. Updated documentation.
  • Removed fields delta_l and delta_h from output in estimate_orf_bayes_factors.
  • Removed deprecated function calls from analysis/profile_construction/get_all_read_filtering_counts, prepare_rpbp_genome, create_base_genome_profile

Added

  • Utility for supressing pystan (or other compiled function) output. For more details see Issue #10.
  • Added limited support for GFF3 specifications, in particular this requires removing the STOP codons from the CDSs and passing the right option to STAR. Prepare_rpbp_genome and create_base_genome_profile modified.
  • If using de_novo, all annotations are concatenated automatically in preparation of running the main pipeline.

Fixed

  • Minor changes to plotting options, typos and/or redundant features in rpbp/analysis/profile_construction/create_rpbp_preprocessing_report and rpbp/analysis/profile_construction/visualize_metagene_profile_bayes_factor. See ISSUE #87. In progress.
  • Added default sjdbOverhang option to star during mapping.

[1.1.11] - 2017-12-08

Removed

  • Removed deprecated function calls from analysis/rpbp_predictions/add_mygene_info_to_orfs, analysis/find_differential_micropeptides, analysis/proteomics/get_orf_peptide_matches and analysis/proteomics/filter_nonunique_peptide_matches

Fixed

  • In create_rpbp_preprocessing_report.create_figures call to filenames.get_riboseq_profiles modified to fix file name reference issue.
  • In create_rpbp_preprocessing_report some figures were referenced before they were created, as a temporary fix, the function create_figures is now called earlier.
  • Minor typos in some of the analysis scripts.

Added

  • Flag added to differentiate between exons file (list of exons for any given transcript), and orfs file (technically, a list of exons per orf). See Issue #59 for more details.

Updated

  • Dependencies to new repo locations.

[1.1.10] - 2017-10-27

Added

  • Reference to helper script to install prerequisite programs. See Issue #75 for more details.

Updated

  • Dependencies to new pymisc-utils and pybio-utils repos. See Issue #74 for more details.

  • Version specification of prereqs

Removed

  • cluster-subcodon-counts. See Issue #78 for more details.

[1.1.9] - 2017-06-15

Added

  • Documentation for using custom alignment files. Please see Issue #73 for more details.

Fixed

  • Documentation links to old ipython notebooks. Please see Issue #71 for more details.

[1.1.8] - 2017-05-22

Fixed

  • Incorrect read filtering report. See Issue #69 for more details.

  • Broken download link for example.

[1.1.7] - 2017-04-03

Fixed

  • Incorrect alignment of ORF data frame and profile matrix. See Issue #54 for more details.
  • ORF coordinates for start codon on exon boundary. See Issue #64 after the reopening for more details.

[1.1.6] - 2017-03-31

Updated

  • Predictions report formatting
  • Guessing read filtering plot tick marks. See Issue #60 for details.

Fixed

  • ORF coordinates when start and stop codons fall on an exon boundary. See Issue #64 for more details.

[1.1.5] - 2017-03-29

Added

  • Documentation for the analysis scripts
  • Documentation for creating reference indices

Fixed

  • Checks that annotation files exist before beginning index creation. See Issue #62
  • Remove unnecessary --tmp argument for pipeline call to predict-translated-orfs. See Issue #63 for more details.

[1.1.4] - 2017-02-22

Removed

  • Unnecessary [analysis] package. Depending on how the package was installed, this sometimes resulted in the scripts not being found. See [Issue #56] (#56) for details.

[1.1.3] - 2017-02-21

Fixed

  • Handling of Stan model paths which include spaces. See Issue #36 for more details. This bug was reintroduced with the commit: "UPD resolve conflicts from dev for version 1.1"

[1.1.2] - 2017-02-15

Fixed

  • Backward-compatiblity syntax in estimate-orf-bayes-factors. See Issue #51 for more details.

Added

  • __version__ and __version_info__ for rpbp package

[1.1.1] - 2017-02-14

Updated

  • Documentation to use pandoc for converting markdown to html

Fixed

  • Broken download link to example files

[1.1.0] - 2017-02-14

This is a rather significant update to the codebase and includes many small changes. Primarily, though, it addresses many installation and system issues.

In particular, thanks to Tonu Margus (@tmargus) for working through many of these issues.

Added

  • Installation instructions for anaconda

Fixed

  • Various installation issues related to calling pip3 from setup.py. Installation of private repositories is now handled via a requirements.txt file.

Removed

  • All uses of (py)bedtools

[1.0.1] - 2017-02-01

Fixed

  • Handling of Stan model paths which include spaces. In particular, this was a problem on OSX. See Issue #36 for more details.

[1.0.0] - 2016-09-05

The initial version, which implements everything in the paper. It was only used on debian-based systems.