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CHANGELOG.md

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Change Log

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

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

[Current]

Added

Fixed

Changed

1.5.3

Added

  • Version checking from cmd line

1.5.2

Fixed

  • seekr_domain_person can run without reference path. (See Issue)

Changed

  • black formatting!

1.5.1

Fixed

1.5.0

Added

  • Unofficial support for different alphabets
  • Additional log transformation option

Fixed

  • Length normalization divisor (length to [length -k +1])
    • Includes a small fix to the length normalization step of the core k-mer counting code. In v1.4.2, k-mer counts were normalized to the number of basepairs in each input sequence. In v1.4.3, k-mer counts are normalized to the number of k-mers in each input sequence ([length_of_sequence] -[k-mer_length]+1). This is a minor change for correctness that should not meaningfully affect results.

Changed

  • Behavior of --log2 argument
    • Includes a redesigned flag to indicate the method of k-mer standardization, and an additional option for k-mer standardization: --log2 [1,2,3] or -l [1,2,3]. These options correspond to log-transforming pre-standardization, post-standardization, or no log-transform, respectively.
    • --log2 post (Default standardization method). This is the same default standardization method used in SEEKR v1.4.2. For a given set of sequences, k-mers are counted, then length normalized (counts per kb of sequence), then z-scores for each k-mer are calculated, and then these z-scores are log2-tranformed. See PMID 31097619 for examples and an in-depth description of the rationale for using log2-transformed z-scores as a default.
    • --log2 none is the same as the no-log transformation option (-nl) of seekr v1.4.2. Here, after k-mers are counted and length-normalized, z-scores are calculated and used without any transformation. This was the approached used in our original SEEKR publication (PMID 30224646).
    • --log2 pre is the additional/new option for standardization. In this approach, k-mers are counted across a set of sequences and then length normalized (counts per kb of sequence). For each k-mer that has a zero-count value in each sequence, a pseudo-count of 1 is added; this allows the k-mer count values to be log2 transformed. Z-scores are calculated after log2-transformation of k-mer counts, and these z-scores can then be used directly for comparisons. In effect, this standardization method is not much different from the default option of --log2 2 (users can compare for themselves). It is, however, a slightly cleaner heuristic. In the time since our original two publications using seekr, we have noted that k-mer counts in the mouse and human transcriptomes tend to follow a log-normal distribution; thus, we currently favor this method of standardization.
  • Includes small updates to “notes” and “Help” sections of README.md

1.4.0

Added

  • seekr_pwms is now callable from the command line
  • seekr_gen_rand_rnas is live

Fixed

  • Updated README
  • Let seekr_visualize_distro handle other matrices

Changed

  • In seekr_domain_pearson, change the way percentiles are calculated, to now be relative to a reference fasta.
  • Improve error when passing a bad release to seekr_download_gencode.

1.3.0

Added

  • seekr_canonical_gencode command line script filters for -001 transcripts.
  • Example integration script in the test directory.
  • Add legacy option to continue using Louvain instead of Leiden.
  • Travis CI automatic push testing.
  • seekr_visualize_distro command makes distribution of r-values.
  • seekr_domain_pearson command line script compares queries and domains in targets.

Fixed

  • Separate fasta.Downloader's url building from file downloading functionality.
  • Convert arguments to integers appropriately in console_scripts.
  • Add help strings to seed docs.
  • 'None' is no longer a part of downloaded file names.
  • Provide unique default path for dumping gml file if one isn't provided.

Changed

  • In seekr_graph, change '-l', '--limit' to '-t', '--threshold'.
  • Set default community detection to Leiden.
  • Remove testing of fasta file downloading.

1.2.0

Added

  • This CHANGELOG was added!
  • Users can see all commands and examples by running "seekr".
  • Users can download fasta files from Gencode with seekr_download.
  • Log2 normalization is now possible and on by default.
  • Users can find Louvain based transcript communities with seekr_graph.
  • Package info is now in __version__.py (modeled after requests). This allows users to do things like seekr.__version__ in a REPL.

Fixed

  • Removed examples of k=7 from README.
  • Stop building list twice while reading fasta data.

Changed

  • All commands now start with 'seekr_' (e.g. 'pearson' is now 'seekr_pearson')
  • README has undergone a large re-write to reflect changes and new features.
  • Console commands produce plain text files by default, instead of binary.
  • Requirements are all described in setup.py requirements.txt has been removed.