VEBA_v1.5.0

Warning:
For this release, use the https://github.com/jolespin/veba/releases/download/v1.5.0/v1.5.0.zip asset not the "Source code" assets as those are out of date.

Release v1.5.0 Highlights:

• Added VeryFastTree to phylogeny.py
• Added --blacklist to compile_eukaryotic_classifications.py
• Added compatibility for antismash_genbanks_to_table.py to operate on antiSMASH v7 genbanks
• Added compile_phylogenomic_functional_categories.py script which automates the methodology from Espinoza et al. 2022 (doi:10.1093/pnasnexus/pgac239)
• Fixed error in annotations.protein_clusters.tsv formatting from annotate.py
• Fixed situation where unbinned.fasta were not added in binning-prokaryotic.py and bad symlinks were created for GFF, rRNA, and tRNA when no genoems were detected.
• Fixed critical error where classify_eukaryotic.py was trying to access a deprecated database file from MicroEuk_v2.

Release v1.5.0 Details

• Cleaned up installation files
• Changed veba/src/ to veba/bin/
• Checked SCRIPT_VERSIONS to VEBA_SCRIPT_VERSIONS which are now in bin/ of conda environment
• Fixed header being offset in annotations.protein_clusters.tsv where it could not be read with Pandas.
• Fixed binning-prokaryotic.py the creation of non-existing symlinks where "'.gff'", "'.rRNA'", and "'*.tRNA'" were created.
• Fixed .strip method on Pandas series in antismash_genbanks_to_table.py for compatibilty with antiSMASH 6 and 7
• Fixed situation where unbinned.fasta is empty in binning-prokaryotic.py when there are no bins that pass qc.
• Fixed minor error in coverage.py where samtools sort --reference was getting reads_table.tsv and not reference.fasta
• Changed default behavior from deterministic to not deterministic for increase in speed in assembly-long.py. (i.e., --no_deterministic --> --deterministic)
• Added VeryFastTree as an option to phylogeny.py with FastTree remaining as the default.
• Changed default --leniency parameter on classify_eukaryotic.py and consensus_genome_classification_ranked.py to 1.0 and added --leniecy_genome_classification as a separate option.
• Added --blacklist option to compile_eukaryotic_classifications.py with a default value of species:uncultured eukaryote in classify_eukaryotic.py
• Fixed critical error where classify_eukaryotic.py was trying to access a deprecated database file from MicrEuk_v2.
• Fixed minor error with eukaryotic_gene_modeling_wrapper.py not allowing for Tiara to run in backend.
• Added compile_phylogenomic_functional_categories.py script which automates the methodology from Espinoza et al. 2022 (doi:10.1093/pnasnexus/pgac239)