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)