Releases · BioJulia/GenomicAnnotations.jl

Iterating over an AbstractLocus now yields the locus itself for simple loci, or the constituent loci for a compound locus (i.e. a Join or an Order). A compound locus wrapped in Complement will yield the constituent loci, individually wrapped in Complement, in reverse order. iscompound(locus) can be used to check whether locus is a compound locus or not. To get the pre-v0.4.3 behaviour of iterating over the individual positions, use eachposition(locus).

Adds GTF support, as well as readgtf(input) and readembl(input).

Adds genedata(gene) and attributes(gene) to make it easier to access the data associated with gene, either as a DataFrameRow referencing the original data in the case of the former, or as a NamedTuple containing copies of the data for the latter.

Adds feature!(gene, f), which can be used to change the feature of a gene.

Various bug fixes.

Closed issues:

gffstring can still merge reverse strand multi-position loci (#16)
gffstring mishandles transpliced genes (#17)
minor issues with headers (#18)

Assets 2

12 Nov 15:14

github-actions

v0.4.2

c39ae6d

v0.4.2

GenomicAnnotations v0.4.2

Diff since v0.4.1

Updated docs and fixed a typo that allowed illegal locus strings to be parsed.

Assets 2

12 Nov 09:36

github-actions

v0.4.1

7e601c8

v0.4.1

GenomicAnnotations v0.4.1

Diff since v0.4.0

Closed issues:

gffstring merges multi-position features (#15)

Assets 2

17 Oct 16:41

github-actions

v0.4.0

345f4d5

v0.4.0

GenomicAnnotations v0.4.0

Introduces a new type-based internal representation of genomic loci. The locus of a gene can still be accessed with locus(gene), which returns an AbstractLocus that should behave similarly to the old locus representation. Hopefully, as long as locus(gene) is being used to access the locus, no code should break, but that cannot be guaranteed.

Diff since v0.3.8

Closed issues: