Package: seqtrie 0.4.0
seqtrie: Radix Tree and Trie-Based String Distances
A collection of Radix Tree and Trie algorithms for finding similar sequences and calculating sequence distances (Levenshtein and other distance metrics). This work was inspired by a trie implementation in Python: "Fast and Easy Levenshtein distance using a Trie." Hanov (2011) <https://stevehanov.ca/blog/index.php?id=114>. It also includes a modified version of the Starcode all-pairs search algorithm (Zorita, Cuscó, and Filion 2015) <doi:10.1093/bioinformatics/btv053>.
Authors:
seqtrie_0.4.0.tar.gz
seqtrie_0.4.0.zip(r-4.7)seqtrie_0.4.0.zip(r-4.6)seqtrie_0.4.0.zip(r-4.5)
seqtrie_0.4.0.tgz(r-4.6-x86_64)seqtrie_0.4.0.tgz(r-4.6-arm64)seqtrie_0.4.0.tgz(r-4.5-x86_64)seqtrie_0.4.0.tgz(r-4.5-arm64)
seqtrie_0.4.0.tar.gz(r-4.7-arm64)seqtrie_0.4.0.tar.gz(r-4.7-x86_64)seqtrie_0.4.0.tar.gz(r-4.6-arm64)seqtrie_0.4.0.tar.gz(r-4.6-x86_64)
seqtrie_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
seqtrie/json (API)
| # Install 'seqtrie' in R: |
| install.packages('seqtrie', repos = c('https://traversc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/traversc/seqtrie/issues
- covid_cdr3 - Adaptive COVID TCRB CDR3 data
- covid_receptors - Adaptive COVID TCRB nucleotide rearrangements
Last updated from:2a8dc5a637. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 245 | ||
| linux-devel-x86_64 | OK | 251 | ||
| source / vignettes | OK | 307 | ||
| linux-release-arm64 | OK | 263 | ||
| linux-release-x86_64 | OK | 228 | ||
| macos-release-arm64 | OK | 254 | ||
| macos-release-x86_64 | OK | 305 | ||
| macos-oldrel-arm64 | OK | 182 | ||
| macos-oldrel-x86_64 | OK | 349 | ||
| windows-devel | OK | 315 | ||
| windows-release | OK | 261 | ||
| windows-oldrel | OK | 250 | ||
| wasm-release | OK | 150 |
Exports:align_searchdist_matrixdist_pairwisedist_searcherasegenerate_cost_matrixhas_sequenceinsertis_validplot_treeprefix_searchradix_forestradix_treeRadixForestRadixTreeresultsingle_gap_searchsizesplit_searchstar_treeStarTreeto_stringto_vector
Dependencies:R6RcppRcppParallelS7
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Alignment search | align_search |
| Adaptive COVID TCRB CDR3 data | covid_cdr3 |
| Adaptive COVID TCRB nucleotide rearrangements | covid_receptors |
| Compute distances between all combinations of two sets of sequences | dist_matrix |
| Pairwise distance between two sets of sequences | dist_pairwise |
| Distance search for similar sequences | dist_search |
| Erase sequences | erase |
| Generate a simple cost matrix | generate_cost_matrix |
| Test sequence membership | has_sequence |
| Insert sequences | insert |
| Validate trie or forest structure | is_valid |
| Plot trie or forest structure | plot_tree |
| Prefix search | prefix_search |
| Radix forest | radix_forest |
| Radix tree | radix_tree |
| RadixForest | RadixForest |
| RadixTree | RadixTree |
| Return a fixed-tree self-similarity result | result |
| Single-gap alignment search | single_gap_search |
| Count stored sequences | size |
| split_search | split_search |
| Starcode-style fixed tree | star_tree |
| StarTree | StarTree |
| Convert a trie or forest to a string | to_string |
| Convert sequences to a character vector | to_vector |
