Version 0.10.0

[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