4

These are NCBI taxonomy ID's rather than anything specific to UniProt. One way to parse them would be using BioPython via Bio.Entrez, for example: from Bio import Entrez def get_taxon_name_from_NCBI_id(id_): Entrez.email = 'name@provider.com' handle = Entrez.efetch(db='taxonomy', id= id_, retmode='xml') records = Entrez.read(handle)[0] ...


2

Here you have the explanation: Suppressed genomes: Several hundred RefSeq bacterial genomes that did not pass assembly or annotation quality validation have been suppressed(RefSeq genome quality criteria). An FTP report file listing the most recent suppressions will be provided soon in the RefSeq FTP site.


1

OK I found the bug. CIBERSORT seems to require tsv files instead of csv files. Plus it doesn't seem to like empty columns


1

That file is actually trivial to parse. You only care about lines that have N=$species, so you can simply do: sed -En 's/.* ([0-9]+): N=(.*)/\1\t\2/p' speclist That will return a tab separated list of taxID and species: $ sed -En 's/.* ([0-9]+): N=(.*)/\1\t\2/p' speclist | head 648330 Aedes albopictus densovirus (isolate Boublik/1994) 10804 Adeno-...


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