vanheeringen-lab/genomepy: Version 0.10.0

Published July 30, 2021 | Version 0.10.0

Software Open

[0.10.0] - 2021-07-30 Added

Annotation class, containing
- regex filter (genomepy.Annotation.filter_regex())
- sanitize functions (genomepy.Annotation.sanitize())
  - option to skip filtering and/or matching the annotation to the genome (also on CLI)
- gene name remapping to various formats (genomepy.Annotation.map_genes())
  - using MyGene.info. Can be queried separately (genomepy.annotation.query_mygene())
- contig name remapping to other provider formats (genomepy.Annotation.map_locations())
- get the annotations, or gene locations, as dataframes (genomepy.Annotation.gtf, bed or gene_coords() respectively)
- get the gene names as a list (genomepy.Annotation.genes("gtf") or genomepy.Annotation.genes("bed"))
genomepy install now attempts to install the NCBI assembly report
NCBI provider also indexes the NCBI genbank_historical summary
genomepy search now shows if the genome has an annotation
- this slows down the results a bit
- to compensate, results are now shown as soon as they are found
- for UCSC, availability of any of the 4 annotations is shown
genomepy annotation shows the first line(s) of each gene annotation.gtf
for developers:
- pre-commit-hooks for linting
- formatting/linting script tests/format.sh (optional argument lint)
- isort & autoflake formatters

Changed

provider module split per provider
ProviderBase overhauled, now called Provider
regex filtering separated from Provider.download_genome
utils module split into utils, files and online
now using loguru for pretty logging
accession search improved
- now finds GCA and GCF accessions
- now ignores patch levels
genomepy install automatic provider selection refactored
- Provider.online_providers returns a generator (faster!)
genomepy install uses a combined filter function (faster!)
genomepy install only zips annotation files if the genome is zipped (with the bgzip flag) (faster!)
NCBI provider should be parsed faster (faster!)
new dependency: pandas
tests no longer format code

Fixed

broken URLs should keep genomepy occupied for less long (check_url will immediately return on "Not Found" errors 404/450) (faster!)
the Genome class now passes arguments to the parent Fasta class
the Genome class now regenerates the sizes and gaps files similarly to the Fasta class and its index (when the genome is younger) (faster!)
somewhat more pythonic tests

Files

Name	Size	Download all
vanheeringen-lab/genomepy-0.10.0.zip md5:73e912422cf135c475037a1275023ef9	834.5 kB	Preview Download

Is supplement to: https://github.com/vanheeringen-lab/genomepy/tree/0.10.0 (URL)