adding ncbi taxonomy dump files
adding mrp folder
various fixes
adding first pass of TreeBASE MRP files
adding additional TreeBASE NeXML files
Updated pruning algorithm. Also, the output is now as follows: treeblock id, "\t", ncbi taxon id, "\t", mrp string
Adding named targets and a recipe for concatenating all tables
adding taxon to species map
this script concatenates TreeBASE MRP files against the MRP matrix induced by the NCBI common tree for all TreeBASE species after normalization
This script collapses TreeBASE subspecies and expands higher taxa to arrive at true species for all source trees. The higher taxon expansion only expands to those species present in TreeBASE, not all of the ones present in the NCBI taxonomy.
make_ncbi_mrp now operates on the true species list, not the taxon list, and it accepts a command line argument to match the correct *.dat files that were produced after normalization instead of the *.txt files from before
This script does the following:
For each TreeBASE NCBI taxon ID:
1. retain if it is a species
2. collapse up to species if a subspecies
3. expand to TreeBASE species if a higher taxon
4. keep higher taxon if no TreeBASE species exist
Makes an MRP matrix from the NCBI common tree for the true species list
adding normalized TreeBASE MRP matrices
adding tnt data files
adding tnt file inclusion commands
adding table with number of characters for each MRP tree block
adding TNT script with all file inclusions
New implementation that should be more memory efficient. Still not enough, but we might not need this anyway.
Added TNT-related targets