The script estimate the phylogenetic entropy and the phylogenetic mutual information across sample given a reference tree and a table of observations
The script user the API https://github.com/albertyw/itol-api to load the reference tree and the estimate of entropy and mutual information on itol web site (http://itol.embl.de/) and produce an output.
With Complements to: Bio python library,iTOL (Interactive Tree of Life), Python API for the Interactive Tree of Life , numpy,scipy, Biopython, pandas python library,GRASS, exelixis ###RUNNING FROM COMMAND LINE python esecutorePhyloHPandas.py [-option] [value]
option -s, -r are mandatory
if -G 0 then also -f -g are mandatory
-H is read only if -G 1
-M is read only if -G 1 and -H different from zero
to obtain the help call "python esecutorePhyloHPandas.py"
-f filename Use this file as the phylogeny file [phylo].
-o filename Use this file to record output
-t filename Use this file to get taxonomic information on some tips and map them in internal node
-s filename Use this file as the sample file [sample].If "-G 1" the file is a CSV that follow darwin archive standard and heading following TWDG
-g filename/string Use this file as the group file [group]/ if "-G 1" is a string that indicates the column in the CSV where to retrive groupping.
-r INT Number of randomizations to use [999]
-x string Two possible strings :"nexml" or "phyloxml" to select the xml output of the results
-h 0 or 1 Boolean to check if you want html output
--QR 0 or 1 Identify linneage present in the Query but not in the Reference (Need found observation to be tagged with "Query" prefix)
--QRC 0 or 1 Collapse branch with only query before analysis
-k 0 or 1 Perform pairwise comparison among all sample to explore variation across all data
-e 0 or 1 Assume that each sampling site have the same sampling effort. This option equalize the weigth of the different sample
--treesimplify Collapse after analysis all descedant nodes that have weighted length to tips less that given [0.01]
-G 0 or 1 Geographic analysis mode: group and sample and potentially taxonomy and tree are all embedded in a CSV that includes also geographical location of observations.
-H INT If data are Geographic, group observation by hexagonal grid of a given span in meters, if zero no gridding is applied and locationID parameters is expected
-M string Cross obseration with a shapecollection -G need to be 1 and -H need to be 0
run example using following call ../esecutorePhyloHPandas.py -f test/Echinodermata.tree -s test/sampleTest -g test/GroupTest -q 1 -r 2 -o xxx -e 0 -k 0
The script is exposed behind a webservice. try http://ecovrp.geodab.eu/wps/testUI/ or for old version visit https://www.biodiversitycatalogue.org/rest_methods/143
Send e-mails to Saverio Vicario (the repo owner) for questions and comments