protr 1.7-4

Improvements

• Improved dependency error handling for similarity calculation functions that use pairwise sequence alignment (#56):
  • Added upfront checks for Biostrings and pwalign dependencies.
  • Now they throw clear errors early if dependency conditions are not met.
  • The new behavior prevents error messages from appearing in results.

protr 1.7-3

Improvements

• For sequence similarity calculations using pairwise sequence alignment, the Biostrings version is now detected at runtime to determine if the pwalign package is needed. This is because the relevant components have been moved from Biostrings to pwalign since Bioconductor 3.19 and Biostrings 2.72.0. This enhancement ensures that protr works properly regardless of the versions of R, Bioconductor, and Biostrings installed (thanks, @ecrespoSSF, #52).

protr 1.7-2

Improvements

• Running citation("protr") now gives better output with the BibTeX citation key. This is improved by adding the key argument to the bibentry() call in inst/CITATION (#49).
• Revised vignette("protr") to fix typos and grammar issues. Updated images to use knitr::include_graphics() chunks, resolving pkgdown 2.1.0 accessibility hints for missing alt text (#50).

protr 1.7-1

New features

• crossSetSim() now gains two new arguments batches and verbose.

  The batches argument allows users to split the similarity computations into multiple batches, which is useful when dealing with a large number of sequences and limited RAM. The verbose argument enables progress updates during the computation. This brings crossSetSim() to feature parity with parSeqSim() (thanks, @ofleitas, #41).

• A new function crossSetSimDisk() has been implemented as a disk-based version of crossSetSim().

  This function follows a similar approach to parSeqSimDisk(), where partial results from each batch are cached on the hard drive and merged at the end. This allows for processing larger protein sequence sets that may not fit into RAM (#41).

protr 1.7-0

New features

• crossSetSim() is added for calculating pairwise similarity between two sets of protein sequence based on sequence alignment (thanks, @seb-mueller, #34).

protr 1.6-3

Bug fixes

• Fixed a minor bug in extractProtFP() and extractProtFPGap() when index = NULL (thanks, @fcampelo #30).

Improvements

• Added a comment about system.file() usage to avoid confusion (thanks, @jonalv #31).
• Replaced previous CI/CD solutions with GitHub Actions workflows.
• Fixed broken or moved links in function documentation and vignettes.
• Replaced the original logo with a new hex sticker logo.

protr 1.6-2

Improvements

• Switched to the tidyverse code style.
• Updated GitHub repository links to reflect the handle change.
• Removed AppVeyor CI due to the frequent Bioconductor dependency installation issues.

protr 1.6-1

Improvements

• Added a new argument batches to parSeqSim(). The new argument supports breaking down the pairwise similarity computation into smaller batches. This is useful when you have a large number of protein sequences, enough number of CPU cores, but not enough RAM to compute and hold all the pairwise similarities in a single batch. Also, use the other new argument verbose to track the computation progress.

New Features

• Added a new function parSeqSimDisk(). Compared to the in-memory version parSeqSim(), this new function caches the partial results in each batch to the hard drive and merges the results together in the end. This could further reduce the memory usage for parallel similarity computations involving a large number of protein sequences.

Bug Fixes

• Fixed an issue in parGOSim() that will create minor numerical inconsistencies in results due to argument matching.

protr 1.6-0

Bug Fixes

• Updated twoGOSim() and parGOSim() to use the latest GOSemSim API for computing GO-based semantic similarity. Issues in the code examples are also fixed. We thank Denisa Duma for the feedback.

protr 1.5-2

Bug Fixes

• Fixed the API endpoint issue (from HTTP to HTTPS) in getUniProt().

Improvements

• Added two new parameters gap.opening and gap.extension to parSeqSim(), allowing more flexible tuning of the sequence alignment for more types of amino acid sequence data. We thank Dr. Maisa Pinheiro for the feedback.
• Added floating TOC and new CSS style in the vignette to improve navigation and readability.