change url to new website from legacy

[adamjohnwright]

This is only once they can handle the larger queries:

https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=list&query=%28reviewed%3Afalse

The pipeline downloads the first file using the following command:
get -N ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz

his file downloads just as before.

The second file download traditionally could be accessed with the
following command:

get -O uniprot-reviewed:no.list.gz https://www.uniprot.org/uniprot/?query=reviewed:no&format=list&force=true&compress=yes

Unfortunately, this one no longer works after the update. I believe the new URL that we should be querying is:

wget -O uniprot-file-test.txt.gz https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=list&query=(reviewed:false)

From this query, we are expecting a list of non-reviewed UniProt ids.

The documentation that the limit for the stream is something like 5 million ( a lot less than the >200 million).

Once they make it so that we can do the query with the non legacy site we should make the switch.

Another way to do this is

Uniprot suggestions:

ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
and use the command below to extract all the accessions:
zgrep '>' uniprot_trembl.fasta.gz | cut -d '|' -f 2

Or, while the legacy site is up (https://legacy.uniprot.org/) you could continue to use your previous command, just replacing www by legacy.