Errors when updating database using make_db.py

[MForofontov]

CDC FTP server anonymous credentials return an error (Python ftplib.error_perm: 530 Login authentication failed) in python and FileZilla, the other one is CDC FTP changed the file name from trimmed.tfa to alltrimmed.tfa thus returning the file not found.

I made changes to the make_db.py to fix both of the issues, by changing ftplib package to urllib, thus using directly the FTP link to download the right file, avoiding the anonymous authentication issue.
Available at : https://github.com/MForofontov/emmtyper/tree/fix-database-updater

[Koen-vdl]

This issue still persists and @MForofontov 's fixed updater is no longer available.

Should anyone still be looking to update the emmtyper db:

mkdir emmtyper_db
curl -o emmtyper_db/alltrimmed.fasta  https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/alltrimmed.tfa
#  (optional) clean up headers
seqkit replace -p ' (.+)' -r '' emmtyper_db/alltrimmed.fasta > emmtyper_db/clean_headers_alltrimmed.fasta
makeblastdb  -dbtype nucl -in emmtyper_db/clean_headers_alltrimmed.fasta -title title -out emmtyper_db/emmtyper_db

Then run emmtyper like this
emmtyper --blast_db emmtyper_db/emmtyper_db --workflow blast --output result.tsv contigs.fasta