vanheeringen-lab/genomepy: [0.13.0] - 2022-06-02

Added

• genomepy search and genomepy genomes can now return the (unfiltered) absolute genome size with argument --size

• changed caching backend to diskcache (thread safe)
• reduced the local cache size of NCBI (by about half)
  • by only storing assembly summary columns actually used by genomepy

• genomepy.Annotation.lengths() to retrieve the gene/transcript lengths.
• genomepy.Annotation.from_attributes() can extract any sub-column that pesky attributes column

• updated Boyle-lab blacklists
• genomepy.Annotation.genes() default changed from bed (commonly containing transcript names) to gtf (gene names)

• blacklists now work with GENCODE
• query_mygene no longer filters input.
• genomepy install with local provider now understands you want the annotation if you pass a path to an annotation