veg / edge-filtering Goto Github PK

Writing the tree_matrix by hand is too cumbersome. It would be nice to have the matrix be generated from within the batch file itself, or write a python script to do it.

 *tree_matrix = {
 *    {1,-1,internal_length,tip_length}
 *    {2,1,internal_length,tip_length}
 *    {3,2,internal_length,tip_length}
 *    {4,3,internal_length,tip_length}
 *    {5,4,internal_length,tip_length}
 *    {6,5,internal_length,tip_length}
 *    {7,6,internal_length,tip_length}
 *    {8,7,internal_length,tip_length}
 *};
 *
 *Each ROW of the matrix defines a sequence to be generated. Columns are as follows
 *
 *[0] : node ID (unique numeric)
 *[1] : the source node for this node (if -1, this is the root)
 *[2] : the edge length between the parent and this node
 *[3] : the amount of within-host evolution that is accrued before the sequence is sampled.

Google Scholar search for HIV-TRACE

• Off-topic, but I found this paper describing the measure of social connectedness using geospatial information. Adapting it for use with a site-level metric could help public health administrators better characterize their districts' behaviors.

Currently there is no "data output folder" where the data will be placed after running through the pipeline, we might want to change that.

Re-add the functionality of GCC and LCC calculator on the GUI and also add it as a command line argument.

Having a Snakemake pipeline that:

1. Runs SimulateSequence.bf
2. Feeds output from SimulateSequence.bf into hivtrace for analysis

would be helpful.

We can later grow this script to include FAVITES