Free method to set NCBI taxonomy dump file names based on a directory.
added a call to EUtils summary() method
Prevent exception in case of empty input dataset
Method to copy from array to array in chunks
Implemented method that embeds Krona source into output directory.
Load and use NCBI merged.dmp file of merged nodes. Load TaxaTree by directory location.
Merged file is tried for mapping taxid argument to TaxaTree.getNode()
into new taxid in case regular lookup failed. Merged is also saved and loaded
from JSON dump, but not yet from SQL dump.
Methods for joining sorted iterators, copying directory tree without timestamps.
Also imported several utility methods from my VICVB source code.
HDF5 based class for final taxonomic predictions.
Remove memory use dependency on the number of input sequences during aggregation.
Time to aggregate is linear function of the number of sequences.
This is done by using HDF5 based dataset for taxonomic predictions,
by accumulating counts for taxids in memory instead of in SQLLite
and by assuming sorted attribute file and using sorted merge join
to match with taxonomic predictions.
Script to generate taxonomic stats for BLAST tabular output.
This includes KRONA charts that can be viewed on a local
file system.