fixed so genomes missing in flextaxd-database are downloaded from...

FOI-Bioinformatics / flextaxd

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

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fixed so genomes missing in flextaxd-database are downloaded from... #63

Closed jaclew closed 1 year ago

jaclew commented 1 year ago

GTDB. The fix includes:

If directory for genome sequences does not exist, notify the user and prompt for creation of directory
Syntax error and mis-spelled variable
Download of the proper file from GTDB (previous: bac120_marker_genes_reps.tar.gz, now: gtdb_genomes_reps.tar.gz)
- I believe the code is not designed to parse the structure for marker_genes.
- Note: The download of GTDB rep-set is slow.
- Suggestion: Download missing accessions using NCBI "datasets" tool