Comments (3)
OK, it's not that simple even for the genome path. For ensembl bacteria, genomes are organised under https://ftp.ensemblgenomes.ebi.ac.uk/pub/bacteria/release-57/fasta/
in bacteria_#_collection
with # in 0-120. The mapping between a bacteria species and its collection is stored in a inconsistently tab-delimited file (there's an extra trailing \t
at the end of each data row).
So the site map class should work like
smap = get_site_map("ftp.ensemblgenomes.ebi.ac.uk")
genome_seq_path = smap.genome_path("Butyribacterium")
genome_seq_path == "fasta/bacteria_15_collection/_butyribacterium_methylotrophicum_gca_001753695/bacteria_15_collection_core_57_110/dna"
Similar behaviour for annotations and alignments.
from ensembllite.
This has been begun with 932c9e3, but is incomplete
from ensembllite.
will revisit this later
from ensembllite.
Related Issues (20)
- SMBE workshop tasks
- installed does not show homology data installation
- alignments should use a directory data store
- alignments command should accept file of genomic coordinates
- MAF files contain duplicated alignment blocks HOT 1
- establish whether duckdb is a viable replacement to sqlite
- ENH: ability to get summary statistics for Ensembl hosted genomes
- download.cfg paths should be relative HOT 1
- ENH: make download experience more robust
- create a docker container for installing EnsemblLite HOT 2
- add option to just get homology info to compara section HOT 1
- DOC: create docs for users
- Initial release on pypi
- investigate process for GitHub action based PyPI releases HOT 3
- install fails on some systems HOT 1
- Restarting install triggers SQL error HOT 1
- Usage on memory limited hardware HOT 2
- download issue HOT 2
- Exporting homolog groups issue HOT 2
- when num CPU is 1, don't use multiprocess
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