Update master #151
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Update master #151
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Also has option to use a datamover queue to make it faster. Added to run.sh
Heavy lifting done in rust now
Two interesting chains 5UQ7_x and 5UQ8_x were previously disqualiified because they are labelled as mRNA. But Rfam finds hits in them, so we want to import them. This commit edits the parser for pdb, and the nextflow process, to allow explicit overriding of type checking for the given chains based on hits from rfam. Seems to work ok, adds 489 new sequences, but still excludes 432 'real' mRNAs
It can parse the output I currently have from the rust code (not yet committed) that selects URSs, genes, experiments and taxids, and looks like it produces sensible results The selection of URSs and genes is not quite right yet, because we're getting lots of stuff with no expression. Think that means we need to use different data, or filter it somehow.
Could probably still use some optimisation, but working for now
Deletes the compiled rust binaries and runs cargo clean
Also introduces parameter for expressionatlas remote
This should collect everything into a single big accession file as well
R21 postrelease patching
Import more pdbe
Fixes RNAcentral/rnacentral-webcode#75. I'm fairly certain the issue with weird common names stems from the parsing that is used to build the rnc_accessions table. For some databases (probably only ENA) we parse the names we are given to extract a common name. This is unreliable. But we don't need to fix that (if it is even possible), because we have a better source taxonomy information, rnc_taxonomy. That table is based of the NCBI taxonomy and uses the official names for species, no need for parsing to extract common names. Thus, we stop using the common_name from rnc_accessions and just use the one from rnc_taxonomy. What this does not change is the usage of the species or lineage from the rnc_accessions table. This should be done, eventually, but before that we have to ensure there is always an entry in rnc_taxonomy for all taxids in xref/accession. This may not be true currently, and is not yet enforced, so I leave those lines alone.
afg1
reviewed
Oct 28, 2022
afg1
reviewed
Oct 28, 2022
afg1
requested changes
Oct 28, 2022
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The only thing I think needs changing before we merge is the default release mode, which I changed to use a query on changes made in the last week. I'll revert that and then I think we're good to go.
A couple of other comments to bear in mind, but I think we can merge
Do not use common names from rnc_accessions
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Generally I try to merge dev for each release.