FlexTaxD v0.4.4

FlexTaxD v0.4.4

New Features

User improvements:

• Initiation of missing directories
• Genome download using NCBI Datasets
• Argument identifiers are more consistent
• Added/modified error messages that are informative
• Improvements to visualization

Database management:

• Announces number of genome-nodes that have matching genomes
• Prompts for automated download of genome-nodes that miss a matched genome
• Removal of genome-nodes without a matched genome
• Renaming of nodes
• Streamlined compilation of FlexTaxD-database to metagenomic classification databases

Bug fixes

• Various code-errors that primarily occurred when working with custom taxonomy or when debugging
• Custom taxonomy files are now parsed properly
• Krakenuniq is no longer supplied with non-existent arguments

FlexTaxD v0.4.3

FlexTaxD V0.4.3

• New Features
  ** Added function that retain defined levels (if merging database does not have levels)
  ** Added function to download genomes from a list of genomes
  ** Added function to export genomes from the database to a list (see above function)

• Bug fixes
  ** Double root id bug resolved
  ** Bug reading GTDB files resolved (Related to taxonomy levels)

• Other
  ** The database now keeps the information from which source the genome annotation is expected to be found (refseq/genbank)

FlexTaxD v0.4.2

FlexTaxD v0.4.2 update

• Tutorial files included
  FlexTaxD now includes some tutorial example files for custom annotation

• Error message update
  Several error messages updated and added

• Download bug
  A bug that occurs occationally with genbank downloads was discovered but is currently unresolved, however to the --force option FlexTaxD now tries to download refseq genomes instead.

FlexTaxD v0.4.1

Bug fixes and one additional supported format (SILVA)

Bug fixes and enhancements

• Error when two names within the tree have identical names.
  • Solved by prompting the optional parents on visualisation
  • Rank level is unique to a link unique(parent, child, rank)
  • Create unique index for each node on export
• SILVA taxonomy support implemented
• Taxonomy files can be read in gzipped format
• --db added as optional parameter choice for -db and --database

FlexTaxD-v0.4.0

Major bottleneck on database merge is solved

Speed increase on merge

• The function to merge for example GTDB with annotations into NCBI was very slow ~15min the main functions was rewritten to allow multiple liftovers in one command which reduced the whole process to about 5s.
• The backside is that there will be no statistics on how many are added/updated

FlexTaxD-v0.3.7

This release contains several minor bug fixes that caused problems in special cases.

details can be found in the branch commits #40

FlexTaxD-v0.3.6

This release contains several minor bug fixes that caused problems in special cases.

details can be found in the branch commits #39

New features

• --skip taxa using file input ( add a file with taxonomies to skip one per row)

A few Error messages are updated

FlexTaxD v0.3.5

Bug fixes and one additional feature

Download representatives

• The option to download the latest representative files from GTDB was added "--representatives"
  • Includes the possibility to specify a full path url to older versions of the representatives --rep_path
  • default rep_path https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/genomic_files_reps/gtdb_genomes_reps.tar.gz

Bug fixes and enhancements

• BadGzipError using python3.7 or earlier
• Bug when using --replace

FlexTaxD v0.3.4

Bug fixes and one additional feature

Database statistics

• An option to print database statistics on number of nodes links and annotated genomes was added --stats

Bug fixes and enhancements

• The kraken2 output option modified in v0.3.3 is not correct and infers a naming error on kraken2 database build - removed and extra columns nessesary added back
• Instead a dbprogram option for "bracken" formatted taxonomy was added
• The script now automatically cleans up tmp files such as library.fna and any added genome, --keep can be used as option to not clean tmp files
• Other minor changes

FlexTaxD v0.3.3

Bug fixes and enhancements

Bug - Script adds a "-" instead of empty column required for kraken2 names and nodes formats and bracken output format -> https://github.com/jenniferlu717/Bracken/issues/126
Bug - script did not allow fasta and fa files to be named without (.fa/.fasta) only .fna files now all types can be with our without ending
Update - better error messages for visualisation function added in 3.2, also new names
      "newick" prints a newick tree to stdout
      "newick_vis"  prints a visualised newick tree to stdout using biopython (requires biopython to be installed)