vanheeringen-lab/genomepy: [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