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driver.py
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driver.py
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'''
Created on Jul 21, 2015
@author: alkpongsema
'''
from MrBayesObj import MrBayesObj
from RAxMLObj import RAxMLObj
from BEASTObj import BEASTObj
from PhyMLObj import PhyMLObj
from jarutils import *
from LeafNorm import LeafNorm
from LogMapPlotter import LogMapPlotter
def makeSeq(n,tree,evomodel):
from SequenceGenerator import SequenceGenerator
seq_dir = 'c:/seqgen/'
for i in range(1,n+1):
shutil.copyfile(seq_dir + tree + ".txt", seq_dir + tree + str(i) + ".txt")
if not os.path.exists(seq_dir + tree + "\\" + tree + str(i) + ".nex"):
tree_gen = SequenceGenerator(tree + str(i),"c:\\seqgen\\" + tree + str(i) + ".txt", evomodel="K-80")
tree_gen.runseq_gen()
shutil.copyfile(seq_dir + tree + str(i) + ".txt", seq_dir + tree + str(i) + "\\" + tree + str(i) + ".txt")
else:
print("SeqGen already run for tree " + str(i) + " - skipping sequence generation.")
if __name__ == '__main__':
#tree = "seagrass"
#tree = "hillisunrooted"
basedir = "c:/seqgen"
runNum = 2
#treeleafgrows = ["leaf01sameedges","leaf02sameedges","leaf04sameedges","leaf06sameedges","leaf08sameedges","leaf10sameedges"]
#treeedgegrows = ["edge01CDE","edge02CDE","edge04CDE","edge06CDE","edge08CDE","edge10CDE"]
treeleafgrowsgtr = ["leaf01sameedgesgtr","leaf02sameedgesgtr","leaf04sameedgesgtr","leaf06sameedgesgtr","leaf08sameedgesgtr","leaf10sameedgesgtr"]
treeedgegrowsgtr = ["edge01CDEgtr","edge02CDEgtr","edge04CDEgtr","edge06CDEgtr","edge08CDEgtr","edge10CDEgtr"]
tree = ""
yeastset = []
'''
for i in range(17,19):
yeaststr = "yeast_" + str(i) + "_genes"
yeastset.append(yeaststr)
'''
#for i in range(len(treeleafgrowsgtr)):
# tree = treeleafgrowsgtr[i]
#for i in range(len(treeleafgrowsgtr)):
# tree = treeleafgrowsgtr[i]
#for i in range(len(yeastset)):
# tree = yeastset[i]
# 1. Sequence generation
#makeSeq(runNum, tree, "GTR")
# convert Beauti
# Create 'treehomes':
'''
for i in range(1,runNum):
if not os.path.exists(basedir + "/" + tree + str(i) + "/" + tree + str(i) + ".nex"):
os.chdir(basedir)
treedir = basedir + "/" + tree + str(i) + "/"
os.mkdir(treedir)
copyTree(tree + str(i),basedir + "/",treedir,False)
else:
print("Sequences already set up for " + tree + str(i) + " - skipping")
'''
#for i in range(len(treeedgegrowsgtr)):
# tree = treeedgegrowsgtr[i]
for i in range(len(treeleafgrowsgtr)):
tree = treeleafgrowsgtr[i]
#for i in range(len(yeastset)):
#tree = yeastset[i]
# 2. Models
#for i in range(1,runNum):
'''
treeBayes = MrBayesObj(tree + str(i))
treeBayes.prep(False)
#treeBayes.prepScript(nst=2,rates="gamma")
treeBayes.prepScript()
treeBayes.run()
treeBayes.runTreeouts()
treeRAxML = RAxMLObj(tree + str(i))
treeRAxML.prep()
treeRAxML.run()
treeRAxML.runTreeouts()
treeBEAST = BEASTObj(tree + str(i))
treeBEAST.prep()
treeBEAST.run()
treeBEAST.runTreeouts()
treePhyML = PhyMLObj(tree + str(i))
treePhyML.prep()
treePhyML.run()
treePhyML.runTreeouts()
'''
# 3. .jar processing and LeafNorms
#models = ["bayes","raxml","BEAST","phyml"]
#models = ["bayes","raxml","BEAST","phyml"]
models = ["BEAST"]
# Generate mean tree, distance files, and distance matrices:
for i in range(1,runNum):
for m in range(len(models)):
model_dir = "/" + models[m] + "/"
treehome = basedir + "/" + tree + str(i) + model_dir
#treefiles = [tree + str(i) + "_bayes_treeout.txt",tree + str(i) + "_raxml_treeout.txt",tree + str(i) + "_phyml_treeout.txt"]
treefiles = [tree + str(i) + "_BEAST_treeout.txt"]
#treefiles = [tree + str(i) + "_bayes_treeout.txt",tree + str(i) + "_raxml_treeout.txt",tree + str(i) + "_BEAST_treeout.txt",tree + str(i) + "_phyml_treeout.txt"]
copyjars(treehome)
if (models[m] == "BEAST"):
findSturmMean(tree + str(i), treehome, models[m], rooted=True)
geoDistanceMatrix(tree + str(i), treefiles[m], treehome, models[m], distlabel = "", rooted=True)
else:
findSturmMean(tree + str(i), treehome, models[m], rooted=False)
geoDistanceMatrix(tree + str(i), treefiles[m], treehome, models[m], distlabel = "", rooted=False)
if not os.path.exists(treehome + tree + str(i) + "_" + models[m] + "_norms.txt"):
ln = LeafNorm(tree + str(i), treefiles[m], treehome, models[m])
ln.makeNormFiles()
# 4. Coordinate discovery for logmaps
#models = ["bayes","raxml","phyml"]
#models = ["bayes"]
models = ["BEAST"]
for i in range(1,runNum):
for m in range(len(models)):
model_dir = "/" + models[m] + "/"
treehome = basedir + "/" + tree + str(i) + model_dir
#treefiles = [tree + str(i) + "_bayes_treeout.txt",tree + str(i) + "_raxml_treeout.txt",tree + str(i) + "_phyml_treeout.txt"]
treefiles = [tree + str(i) + "_BEAST_treeout.txt"]
#treefiles = [tree + str(i) + "_raxml_treeout.txt",tree + str(i) + "_BEAST_treeout.txt",tree + str(i) + "_phyml_treeout.txt"]
logplot = LogMapPlotter(tree + str(i), treefiles[m], treehome, models[m], rooted=True)
#logplot = LogMapPlotter(tree + str(i), treefiles[m], treehome, models[m], rooted=False)
logplot.split_topos()
logplot.make_centres()
logplot.make_coords()
#os.remove(tree + str(i) + "_" + models[m] + "_allcoords.r")
#os.remove(tree + str(i) + "_" + models[m] + "_allcoords_norm3D.r")
logplot.plot_coords_all()
#logplot.plot_coords_quads()
# To delete directories and their contents:
#shutil.rmtree(treehome + "quadrant_plots")
#orderByLogMap(tree + str(i), basedir + "/" + tree + str(i), models[m], best=False, orderby=1, bynorm=False)
#orderByLogMap(tree + str(i), basedir + "/" + tree + str(i), models[m], best=False, orderby=1, bynorm=True)