[0.11.0] - 2021-11-18

Added

• extened docstrings
• GENCODE support (GENCODE gene annotations with UCSC genomes)
  • only contains the main chromosomes, no scaffolds or alternate haplotypes.
  • only contains 4 assemblies (2 mouse, 2 human)
  • excellent annotations for these regions & species though!
• Ensembl's GRCh37 can now be downloaded through genomepy
• Local fasta/gtf/gff(3)/bed file support
  • you can install a local genome and/or annotation by providing local path(s) to genomepy install
    • if annotation downloading is requested, but not annotation path is provided,
      a gtf/gff(3) annotation will be sought in the genome's source directory.
• Annotation.gtf_dict creates a dictionary for any key-value pair in the GTF columns or attribute fields!
  • e.g. Annotation.gtf_dict("seqname", "gene_name")

Changed

• Genome.track2fasta can now ignore comment lines (starting with #)
• Genome.track2fasta will skip header lines (a warning will be printed)
• Genome.track2fasta will ignore regions that cannot be parsed (a warning will be printed)
  • these fixes should improve gimme scan performance and feedback
• UCSC annotation conversion tool settings tweaked. Better results with source gff files.
• Ensembl now uses HTTP instead of FTP (in some cases). This improves stability on some servers.
• tweaked search result alignment for clarity
• explained UCSC annotations in the README
• better file path handling (relative paths, user home and variables are expanded)
• Annotation now accepts a file/directory/genomepy name as first argument.
  • this merges 2 arguments into one.
• Annotation.map_genes now works without a README file
  • you can now set Annotation.tax_id manually.

Fixed

• Ensembl annotations from previous releases can now be downloaded as intended.
• Genome.track2fasta will skip regions that clearly dont make sense (start>end, and start<0)