install_databases.py downloads unneeded hidden files

[jowodo]

• pharokka version: 1.3.2
• Python version: 3.10.12 (from conda)
• Operating System: Oracle Linux 8.8

Description

I want to download the databases, which worked, but I got some (Ignoring) warnings and extra filesystem related files, which could be avoided in the next release.

What I Did

$ install_databases.py -o scratch/mirror/pharokka/1.3.2
PHROGs Databases are missing.
VFDB Databases are missing.
CARD Databases are missing.
PHROGs Annotation File is missing.
INPHARED Mash Annotation File is missing.
INPHARED Mash Sketch File is missing.
Some Databases are missing.
Downloading Pharokka Database
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  242M  100  242M    0     0  2236k      0  0:01:50  0:01:50 --:--:-- 2240k
tar: Ignoring unknown extended header keyword 'SCHILY.fflags'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.FinderInfo'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.quarantine'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.macl'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.quarantine'

$ ls /scratch/mirror/pharokka/1.3.2/
.DS_Store                           CARD_h                              phrogs_profile_db.index             vfdb
._.DS_Store                         CARD_h.dbtype                       phrogs_profile_db_consensus         vfdb.dbtype
._5Jan2023_data.tsv                 CARD_h.index                        phrogs_profile_db_consensus.dbtype  vfdb.index
._5Jan2023_genomes.fa.msh           VFDB_setB_pro.fas                   phrogs_profile_db_consensus.index   vfdb.lookup
5Jan2023_data.tsv                   aro_index.tsv                       phrogs_profile_db_h                 vfdb.source
5Jan2023_genomes.fa.msh             phrog_annot_v4.tsv                  phrogs_profile_db_h.index           vfdb_h
CARD                                phrogs_db                           phrogs_profile_db_seq               vfdb_h.dbtype
CARD.dbtype                         phrogs_db.dbtype                    phrogs_profile_db_seq.dbtype        vfdb_h.index
CARD.index                          phrogs_db.index                     phrogs_profile_db_seq.index
CARD.lookup                         phrogs_profile_db                   phrogs_profile_db_seq_h
CARD.source                         phrogs_profile_db.dbtype            phrogs_profile_db_seq_h.index

I suggest not downloading .DS_Store files and hidden backup files (._*).

Thanks for your time!

PS: the issue templates says 'phrokka' instead of 'pharokka' in the first line.

[gbouras13]

Hi @pur80a,

Thanks for this (and the typo catch) - Pharokka will soon have a new version 1.4.0 with a lot of new features, including an updated database. Hopefully not too long to wait!

George

[jowodo]

Great! Thanks!