Central location to deposit current work on keys for taxonomy; revisions, NCBI issues, etc. Then I don't have to search every repository I have for each version.
Go here for the latest versions
To generate keys and lists. Hakai-rosetta folder with workflow for rosettas. Older scripts largely outdated but collected here for reference when reviewing old projects.
First, we need to run CRABS from the CRABS folder to generate the initial database.
Currently (2023-09-27) the workflow needs updated here as we should create a crabs database in this directory.
The latest version was generated from a CRABS database from my chapter 1 repository.
Right now there are a few possible methods in the folder for extracting NCBI info.
00 scripts are to process initial downloads/etc.
extract-taxonomy would be from a NCBI summary file
extract-taxonomy_tinyseq would be from an NCBI tinyseq file
extract_ncbinum is from the crabs database FASTA
01_fish_ncbi-efetch-taxonomy.py takes the output from extract-ncbinum or any txt file that's a list of ncbi numbers to query ncbi for taxonomy using efetch. Currently it does not have a method to handle problems from NCBI and will sometimes throw an error and stop the loop. But there is nothing wrong with the record, it just needs to be restarted.
01a_trimlist.py will trim the list of accession numbers for when efetch-taxonomy hangs up and stops. This way the script can be easily restarted and won't have to rewrite numbers
02_fish_ncbi2worms.Rmd Goes through the output from efetch taxonomy to: indicate gene(s) from accession number, generate a verbatim name to match, match with worms
latest lists
ncbi
BC = lists from partners in BC, OBIS/GBIF pulls filtered to latitudes
Hakai = blast database and rosetta process 2022rosetta > current draft is where output from scripts go, then are moved to latest-keys. Includes intermediate files, best to use latest-keys instead > problems: contains output from the first few scripts in the rosetta process. includes outstanding problems and conflicts currently being explored. > taxize : initial taxize output before merging with each other and resolved problems. separated by phylum. >> this means if only one phyla needs updated the whole database doesn't need run through taxize again
Fish = right now (august 2022) most lists are in scratchwork as I confirm which ones are valid/useful/not outdated. Mostly copypasted from previous projects
Fossil = 2021 extraction of BC fossils from PaleoBioDB
Invertebrates = same as fish
pdfs with species lists for regions