https://github.com/biojulia/genomicannotations.jl - v0.4.5

GenomicAnnotations v0.4.5

Diff since v0.4.4

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

https://github.com/biojulia/genomicannotations.jl - v0.4.4

GenomicAnnotations v0.4.4

Diff since v0.4.3

Closed issues: - [Feature Request] Support for GTF format! (#12) - Sequence section of .gbk output is non-standard? (#19)

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

https://github.com/biojulia/genomicannotations.jl - v0.4.3

GenomicAnnotations v0.4.3

Diff since v0.4.2

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)

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

https://github.com/biojulia/genomicannotations.jl - 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.

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

https://github.com/biojulia/genomicannotations.jl - v0.4.1

GenomicAnnotations v0.4.1

Diff since v0.4.0

Closed issues: - gffstring merges multi-position features (#15)

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

https://github.com/biojulia/genomicannotations.jl - v0.4.0

GenomicAnnotations v0.4.0

Diff since v0.3.8

Closed issues: - Can GenomicAnnotations.jl deal with multi-exon genes? (#9) - Type piracy of Base breaks package in 1.11 (#14)

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

https://github.com/biojulia/genomicannotations.jl - v0.3.8

GenomicAnnotations v0.3.8

Diff since v0.3.7

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

https://github.com/biojulia/genomicannotations.jl - v0.3.7

GenomicAnnotations v0.3.7

Diff since v0.3.6

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

https://github.com/biojulia/genomicannotations.jl - v0.3.6

GenomicAnnotations v0.3.6

Diff since v0.3.5

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

https://github.com/biojulia/genomicannotations.jl - v0.3.5

GenomicAnnotations v0.3.5

Diff since v0.3.4

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

https://github.com/biojulia/genomicannotations.jl - v0.3.4

GenomicAnnotations v0.3.4

Diff since v0.3.3

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

https://github.com/biojulia/genomicannotations.jl - v0.3.3

GenomicAnnotations v0.3.3

Diff since v0.3.2

Merged pull requests: - bugfix for delete!(genes) (#10) (@hsianktin)

Closed issues: - Having location field in genes (#11) - Trouble loading .gb file downloaded via benchling (#13)

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

https://github.com/biojulia/genomicannotations.jl - v0.3.2

GenomicAnnotations v0.3.2

Diff since v0.3.1

Closed issues: - GzipDecompressorStream not defined (#8)

- Julia
Published by github-actions[bot] over 4 years ago

https://github.com/biojulia/genomicannotations.jl - v0.3.1

GenomicAnnotations v0.3.1

Diff since v0.3.0

- Julia
Published by github-actions[bot] over 4 years ago

https://github.com/biojulia/genomicannotations.jl - v0.3.0

GenomicAnnotations v0.3.0

Diff since v0.2.3

- Julia
Published by github-actions[bot] almost 5 years ago

https://github.com/biojulia/genomicannotations.jl - v0.2.3

GenomicAnnotations v0.2.3

Diff since v0.2.2

Closed issues: - Error when loading genebank file from NCBI (#7)

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/genomicannotations.jl - v0.2.2

GenomicAnnotations v0.2.2

Diff since v0.2.1

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/genomicannotations.jl - v0.2.1

GenomicAnnotations v0.2.1

Diff since v0.2.0

Updated to a Reader/Writer interface for IO, and moved GenBank and GFF IO to separate submodules.

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/genomicannotations.jl - v0.2.0

GenomicAnnotations v0.2.0

Diff since v0.1.6

- Julia
Published by github-actions[bot] about 5 years ago

https://github.com/biojulia/genomicannotations.jl -

Updated to the new (v0.20) DataFrames API. Fixed a bug when reading files with empty lines.

- Julia
Published by kdyrhage over 5 years ago

https://github.com/biojulia/genomicannotations.jl - v0.1.5

GenomicAnnotations v0.1.5

Diff since v0.1.4

Merged pull requests: - Install TagBot as a GitHub Action (#3) (@JuliaTagBot) - Parsegff (#4) (@kdyrhage)

- Julia
Published by github-actions[bot] almost 6 years ago

https://github.com/biojulia/genomicannotations.jl - v0.1.4

v0.1.4 (2019-12-12)

Diff since v0.1.2

- Julia
Published by julia-tagbot[bot] over 6 years ago

https://github.com/biojulia/genomicannotations.jl -

Updated for DataFrames v0.19.0.

- Julia
Published by kdyrhage almost 7 years ago

https://github.com/biojulia/genomicannotations.jl -

Some updates: - Added GZip.jl as a dependency, and updated readgbk to read gzipped files. - Allowed parsing of loci with "^" in the position string - Added special cases to @genes. - iscds expands to :feature == "CDS" - get(s::Symbol, default) expands to get(gene, s, default) - When providing just a symbol (such as in @genes(chr, :pseudo)), missings will be treated as falses.

- Julia
Published by kdyrhage over 7 years ago

https://github.com/biojulia/genomicannotations.jl - Initial release

- Julia
Published by kdyrhage over 7 years ago