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Changelog

Development

0.8.0 (2019-07-04)

Fixed

  • Broken test due to platform differences in Path.glob sorting.

Added

  • User can specify to use start or end tokens optionally.

Removed

  • Removed one_hot_encoding. The user can do that pretty easily if needed. E.g. see scatter in PyTorch.

0.7.0 (2019-06-22)

Added

  • Properties to access the integer encodings of special tokens. (35cae2a)
  • Alphabet.encoded_start
  • Alphabet.encoded_end
  • Alphabet.encoded_padding
  • Remove uniprot dataset creation. (e233162)
  • Simplify index handling for GenomicDataset. (3213a9e)

0.6.1 (2019-06-10)

Added

  • Updated package management so gcgc is easier to use with other version of torch.

0.6.0 (2019-04-04)

Added

  • Ability for kmer size to be passed to an alphabet.

0.5.2 (2019-03-21)

Added

  • Add Dockerfile and docker-compose.yml for development.
  • EncodedSeq.shift, which will shift sequence by an offset integer.
  • EncodedSeq.from_integer_encoded_seq will take a list of integers and an alphabet and return an EncodedSeq object.
  • Add the ability to apply a function to the rollout_kmers yielded values.

Changed

  • Alphabet special characters are now located at the start, rather than the end, of the letters and token sequence.

0.5.1 (2019-01-09)

Added

  • Add extra css to make underline links in articles.
  • Exit if the download directory doesn't exist in the call to download organism.
  • Wording improvements in docs.

0.5.0 (2018-12-31)

Added

  • Include seq_tensor_one_hot in the PyTorch Parser.
  • Added a GCGCRecord.encoded_seq property.
  • New gcgc.random module to start holding sequence data.
  • New gcgc.rollout module to handle working through chunks of sequences.
  • rollout_kmers will roll out kmers.
  • rollout_seq_features will roll out the SeqFeatures from a SeqRecord.
  • EncodingAlphabet now can optionally take a gap_characters set of characters to add to the alphabet letters. It also takes add_lower_case_for_inserts which will duplicate the alphabet, but convert the letters to lowercase.

Changed

Fixed

  • Fixed bug in GenomicDataset.from_path where it still referred to init_from_path_generator.

0.4.0

Added

  • EncodedSeq now supports iterating through kmers, see EncodedSeq.rollout_kmers for options.
  • GCGC is citable.
  • GCGC now has a CHANGELOG.md.