Use the accompanying example files by changing to the correct
directory:
It is always a good idea to validate the configuration file to make
sure it is correct:
java ooc.Validate prop.xml |
It is valid if nothing is returned, else one row per error is
printed. Then index the data in the darwin database file
(
db.drw) and the
NCBI Taxonomy files (
names.dmp and
nodes.dmp):
java softparsmap.DataSourceXmlNcbiTaxonomy prop.xml example |
This index file must be rebuilt after changing the database file or
the NCBI files.
Then root the gene trees in
./trees/ by mapping
them on to the tree of life:
java softparsmap.Compute prop.xml root_example unrooted |
The rooted trees with in-paralogous removed are written in to
./target/.
These trees and their rooting are described in the softparsmap paper
[1] and to compute the final map type
java softparsmap.Compute prop.xml map_example rooted |
The files in
target ending with
.tree contains the rooted trees in Newick format
and the files ending with
.info contains two rows
from the mapping. The first row is the rooted gene tree in Schreiber
format and the second row is an array mapping to the internal nodes.
If the value is 'D' the corresponding internal node is duplicated.
You can use this on your own data if you replace
db.drw with your own sequence information, and
the trees in trees/* with your own, being
careful to copy the formats of the example data.
More details below.