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Releases: psipred/s4pred

v1.2.0: Supports outputting PSIPRED HFORMAT

07 Jan 07:08
@limitloss limitloss
v1.2.0
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v1.2.0: Supports outputting PSIPRED HFORMAT Latest
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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.
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v1.1.0

04 Jan 04:43
@limitloss limitloss
v1.1.0
a6cf058
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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.
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v1.0.0

03 Jan 23:51
@limitloss limitloss
v1.0.0
df513b8
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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.
Assets 2
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