v1.2.0: Supports outputting PSIPRED HFORMAT

Added

• Functionality to output files with the PSIPRED HFORMAT (.horiz files) for parity with PSIPRED's H and V formats. Also allows easier future incorporation of S4PRED into the PSIPRED Workbench.
• 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.

v1.1.0

1.1.0 - All Changes

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

• Shift to using the Biopython FASTA file parser.
• Update run_model.py to run and save batches of sequences from a single input FASTA file.
• 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.

v1.0.0

All Changes Since Init

Added

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

Changed

• Slimmed down the contents of the Citation section in the README.
• Fixed badges and made them visible.
• Corrected invalid username references in python files.
• 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.

To Do

• Shift to using the Biopython FASTA file parser.
• Update run_model.py to run and save batches of sequences from a single input FASTA file.