GeneFinder v0.7.0

Diff since v0.6.1

Breaking changes

This add the refactor ORFI and a new way to predict Ribosome Binding Sites (RBSs) similar to Prodigal and score an ORF based on that

Merged pull requests: - Ribosome Binding Sites motifs (#37) (@camilogarciabotero)

- Julia
Published by github-actions[bot] about 1 year ago

GeneFinder v0.6.1

Diff since v0.6.0

Merged pull requests: - Rename ORF to ORFI (#36) (@camilogarciabotero)

- Julia
Published by github-actions[bot] over 1 year ago

GeneFinder v0.6.0

Diff since v0.5.0

- Julia
Published by github-actions[bot] almost 2 years ago

GeneFinder v0.5.0

Diff since v0.4.0

Merged pull requests: - Moving ORF as an AbstractGenomicInterval{T} (#34) (@camilogarciabotero) - Refactor docs and improve chapter readability (#35) (@camilogarciabotero)

Closed issues: - Using score to filter what getorfs delivers (#33)

- Julia
Published by github-actions[bot] almost 2 years ago

GeneFinder v0.4.0

Diff since v0.3.0

Merged pull requests: - Bump julia-actions/setup-julia from 1 to 2 (#29) (@dependabot[bot]) - Improve interface for further methods (#32) (@camilogarciabotero)

Closed issues: - The iscoding should be more generic. (#30)

- Julia
Published by github-actions[bot] about 2 years ago

GeneFinder v0.3.0

Diff since v0.2.0

Merged pull requests: - Scoring field in the ORF structs (#26) (@camilogarciabotero) - Decoupling findorfs method (#27) (@camilogarciabotero) - Add a new ORF finder method algorithm using BioMarkovChains.jl (#28) (@camilogarciabotero)

- Julia
Published by github-actions[bot] about 2 years ago

GeneFinder - v0.2.0

GeneFinder v0.2.0

Diff since v0.1.0

Breaking changes

A more stable ORF type that asserts for incorrect ORFs.
Extended Base.getindex method to better handle ORF enabling: seq[orf] regardless of the ORF strand.
The write_* API is much more stable and its been rewriten to handle IOStreams and IOBuffers as well.
The new record_orfs_fna and record_orfs_faa methods intearact with the FASTX interface.
Codebase has been reduced. Direct String manipulation is not enabled for findorfs and get_* methods.
Docstrings have been updated following method updates.
Better tests and now Aqua.jl is used for several tests as well.

Merged pull requests: - Refactor ORF main type, update entire writting API and other general changes (#23) (@camilogarciabotero)

- Julia
Published by github-actions[bot] over 2 years ago

GeneFinder - v0.1.0

GeneFinder v0.1.0

Diff since v0.0.23

Merged pull requests: - Bump actions/checkout from 3 to 4 (#22) (@dependabot[bot])

- Julia
Published by github-actions[bot] over 2 years ago

GeneFinder - v0.0.23

GeneFinder v0.0.23

Diff since v0.0.22

Merged pull requests: - General clean up (#21) (@camilogarciabotero)

- Julia
Published by github-actions[bot] over 2 years ago

GeneFinder - v0.0.22

GeneFinder v0.0.22

Diff since v0.0.21

- Julia
Published by github-actions[bot] almost 3 years ago

GeneFinder - v0.0.21

GeneFinder v0.0.21

Diff since v0.0.20

Merged pull requests: - Adding frame information to ORFs (#20) (@camilogarciabotero)

- Julia
Published by github-actions[bot] almost 3 years ago

GeneFinder - v0.0.20

GeneFinder v0.0.20

Diff since v0.0.19

Merged pull requests: - Bump actions/checkout from 2 to 3 (#18) (@dependabot[bot]) - Bump codecov/codecov-action from 2 to 3 (#19) (@dependabot[bot])

- Julia
Published by github-actions[bot] almost 3 years ago