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CHANGELOG.md

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Change Log

All notable changes to the pbiotools package will be documented in this file.

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

[Unreleased] - started 2023-09

[4.0.2] - 2023-09

Removed

  • math_utils.get_kth_fold (more_itertools)

[4.0.1] - 2023-02

Fixed

  • Handling of missing GTF attributes

Changed

  • Docstrings (Rp-Bp API)

[4.0.0] - 2023-01

Removed

  • Python 3.6 (requires Python >= 3.7)
  • pybedtools, pyyaml
  • parse-meme-names

[3.0.0]

Added

  • PyPI installation
  • Bioconda installation

Removed

  • PyStan dependency
  • Pickling of Stan models
  • Periodic offsets with the best Bayes factor mean largest_bf_
  • pbiotools.ribo (now in Rp-Bp)

Fixed

  • Variance estimates bayes_factor_var (metagene profiles)

[2.0.0]

API change.

Changed

  • pbio to pbiotools

Added

  • GitHub CI workflow, pre-commit

[1.0.0] - 2019-10-26

This is a major version change due to reorganisation of the package structure, obtained by merging the defunct pymisc-utils (see pyllars) and riboseq-utils. The package name has been changed from bio_utils to pbio to reflect this change in API.

Changed

  • Changed star_utils to pgrm_utils and add functions for cmd parser to call flexbar
  • Rename ORF files in ribo.ribo_filenames, adjust ORF labels in ribo.ribo_utils
  • Configure setup() using setup.cfg

Fixed

  • Missing parameters in function calls, hard coded defaults
  • Missing argument for BED6 in bed_utils.get_all_bed_sequences.
  • Call to shell_utils in bam_to_wiggle.py.

Added

  • New file for ORF labels in ribo.ribo_filenames
  • Add backend option to parallel, enabling to resort to the old multiprocessing backend.
  • Various functionality to bam_utils to filter BAM files by tag, flag; rewrite remove_multimapping_reads into remove_multimappers, the former to be deprecated.
  • Added to bio_programs create_init_ribo_track.py.

[0.2.6] - 2018-03-14

Added

  • Added to bio_programs bed_to_bigBed, run_signalp and run_tmhmm.

Removed

  • Removed deprecated function calls from bio_programs parse_meme_names, create_mygene_report, get_all_utrs, get_read_length_distribution, count_reads and count_aligned_reads.
  • Removed deprecated function calls from bed_utils.
  • Removed deprecated function calls from fastx_utils, bam_utils.
  • Removed deprecated function call from gtf_utils.

Fixed

  • Minor changes to bio_utils.plotting.plot_read_length_distribution, see ISSUE #87.

Added

  • Added partial support for GFF3 specifications, in particular this requires removing the STOP codons from the CDSs. Reference annotations file with gff extension are now treated as GGF3.
  • Handling of additional options passed to star via arguments to star_utils.

[0.2.5] - 2017-12-08

Updated

  • Removed deprecated function call from mygene_utils

[0.2.4] - 2017-10-26

Updated

  • Version specifications for prereqs

[0.2.3] - 2017-07-27

Updated

  • Updated download-srr-files to use misc.shell_utils and http rather than ftp

[0.2.2] - 2017-06-14

Fixed

  • References to old gtf functions in misc.bio

[0.2.1] - 2017-06-14

Fixed

  • All references to misc.bio and misc.bio_utils. Please see Issue #1 in the new repo for more details.

[0.2.0] - 2017-05-31

This is a new version which moves the project from Bitbucket to GitHub. Additionally, the other utilities (misc.***) have been completely removed. They will be added to a new pymisc-utils repository.

[0.1.6] - 2017-05-10

Fixed

  • Missing import in counting alignments for bam files

[0.1.5] - 2017-05-09

Updated

  • get-read-length-distribution script to handle bam, fasta and fastq files. See the bio docs for more details.

[0.1.4] - 2017-05-09

Removed

  • bed, bam and gtf helpers from bio.py. These had already been deprecated for quite some time.

[0.1.3] - 2017-03-30

Added

  • Script to remove duplicate entries from bed files. See the bio docs for more details.

[0.1.2] and previous versions

The initial versions have not been documented in the change log.