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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

This format is based on Keep a Changelog, and this project would like to in spirit adhere to Semantic Versioning.

[1.2.5] - 2023-10-02

Changed

  • README.md to include download links for the real-labelled datasets.

[1.2.4] - 2023-01-28

Added

  • Option to supply a file prefix with a new command line option for run_model.py,

Changed

  • README.md to reorder the About section, add a section to describe the new prefix option, and a section describing the new method's PSIPRED Workbench availability.

[1.2.3] - 2023-01-16

Added

  • Option to save the results in a secondary file format. E.g. a sequence prediction can be saved as both ss2 and horiz in the same run without having to run twice.

Changed

  • README.md to correct broken links and improve clarity.

[1.2.2] - 2023-01-16

Changed

  • Fixed bug in run_model.py causing FASTA output to fail silently.
  • Added single letter options for command line arguments.

[1.2.1] - 2023-01-16

Changed

  • README.md to correct broken links and improve clarity.
  • s4pred.svg from an inkscape SVG to a standard SVG so its not bloated with metadata and other unneccesary information.

[1.2.0] - 2023-01-06

Added

  • Functionality to output files with the PSIPRED HFORMAT (.horiz files).
  • An example of the output in example/1qys.horiz.
  • Details to the README.md regarding the output format.

Changed

  • Fixed version number of output ss2 file header in run_model.py.
  • README.md to correct typos and improve clarity.

[1.1.0] - 2023-01-04

Added

  • Dependency on Biopython, specifically the SeqIO module.
  • Example of a FASTA file containing multiple sequences, with example/multi_seqs.fas.
  • Added line to README.md regarding the RCSB PDB no longer providing updated secondary structure flat files (i.e. ss.txt.gz).
  • Added descriptions of new output options.
  • example/1qys_ss_conf.fas included as an example of adding confidence scores to the .fas format.
  • example/multi_seqs.fas for examples of predicting from a file containing more than one sequence.

Changed

  • Behavior of utilities.py and run_model.py so they now parse and predict multiple sequences from a single FASTA file.
  • utilities.py uses a new wrapper around the Biopython parser.
  • run_model.py refactored to predict from multiple sequences in a single FASTA files.

To Do

  • Add name and ID post-processing after Biopython read to improve the downstream file naming.
  • Add separate inference script for large dataset processing with batches.

[1.0.0] - 2023-01-03

Added

  • README section on the inference code.

Changed

  • Corrected invalid username references in python files.

[0.0.1] - 2023-01-03

Added

  • This CHANGELOG file.
  • README now contains references and descriptions of: -- CHANGELOG. -- Contact for main developer @limitloss.

Changed

  • Slimmed down the contents of the Citation section in the README.
  • Fixed badges and made them visible.
  • Widened the banner SVG file, and the corresponding PNG banner image file.

Removed

  • Removed hench deleted files from main branch's history, drastically reducing the pack-file size.