import load_synth_extract
from plants_all import studytreelist
if __name__ == "__main__":
from stephen_desktop_conf_TEMP import *
synthottolid="10218"
studytreelist = ["2539_6294"]
print "loading synthottolid:",synthottolid
print "loading studytreelist:",studytreelist
generallogfileloc = studytreelist[0]+".log"
ttfntreefn = studytreelist[0]+".tre"
load_synth_extract.run(dott,dload,studyloc,studytreelist,javapre,
treemloc,generallogfileloc,dsynth,synthottolid,ttfntreefn,[True])
"41_1396", #Feddea
"82_5792", #Campanula , very non monophyletic campanula
"932_1831" #Goodeniaceae, tons of non monophyly
]
studytreelistTF = [True] * len(studytreelist)
if __name__ == "__main__":
treemloc = "treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar" #treemachine location
javapre = "java -Xmx8g -jar" #java running information
dott = "example/asterales_taxonomy.db" #database location for taxonomy
taxfile = "example/aster/taxonomy.tsv" #location of taxonomy loading file
synfile = "example/aster/synonyms.tsv" #location of synonyms file
dload = "example/asterales_loading.db" #database location for loading studies
dsynth = "example/asterales_synth.db" #databsae location for synthesis
synthottolid = "1042120" #ott id for starting synthesis
treefn = "example/asterales_synth.tre" #filename for tree
generallogfileloc = "example/logfile" #log file for spitting out lots of information
studyloc = "example/nexsons/" #location for the nexsons
delete_database(dott)
print "loading taxonomy"
load_taxonomy(treemloc, javapre, dott, taxfile, synfile)
print "loading synthottolid:", synthottolid
print "loading studytreelist:", studytreelist
load_synth_extract.run(dott, dload, studyloc, studytreelist, javapre,
treemloc, generallogfileloc, dsynth, synthottolid,
treefn, studytreelistTF)
