tidy processing of biological sequences in R
Updates for the CRAN god. Fixed random_sq()
out-of-bounds possible problem, so there may be differences in sequences generated using the same seed in this and previous versions.
random_sq()
correctly ignores now "*" and "-" values while computing number of letters to draw fromSequence
and ProtoSequence
classesExpanded on v1.0.0, having implemented functions paste()
and collapse()
that allow the user to connect multiple sequences into one. Also made some optimization within C++ using templates, speeding up translate()
and complement()
functions significantly. Lastly, added support for object from bioseq
package.
interpret_as_stop
from translate()
function, as it is not feasible to implement well-working translation rules for tables with ambiguous codons (27, 28 & 31)paste()
(a method for sq
class)collapse()
bioseq
package, i.e. bioseq_aa
, bioseq_dna
and bioseq_rna
translate()
to have codon tables created in compile time; this reduced execution time of translate()
by 95%
complement()
to have tables created in compile time; this reduced execution time of complement()
by 85%
random_sq()
actually use seed
parameter while generating sequencesNot much different to the previous, v0.5.0 release. Features a stable API with working C++ Operation
interface.
From now on all future releases will be named according to semantic versioning practices. API changes and bugfixes will be listed as well.
Most of the intended functionalities are there, we don't expect API to change much if at all. Still working on rewriting crucial (and not-so-crucial) code in C++ and better test coverage (though API is already quite well covered).