def makeSeq(n,tree):
seq_dir = 'c:\\seqgen\\'
seq_tree_dir = 'c:\\seqgen\\' + tree + '\\'
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")
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.")
from my_helper import *
import shutil
from make_rMDSscript import make_rMDSscript
if __name__ == '__main__':
tree = ""
#tree = "basenew" + "_raxml"
tree_data = "\\" + tree
seq_dir = 'c:\\seqgen\\'
seq_tree_dir = 'c:\\seqgen\\' + tree + '\\'
bayes_exe = 'mrbayes_x64.exe'
if not os.path.exists(seq_dir + tree + "\\" + tree + ".nex"):
tree_gen = SequenceGenerator(tree,"c:\\seqgen\\" + tree + ".txt")
tree_gen.runseq_gen()
else:
print("SeqGen already run - skipping sequence generation.")
# add code to move Mr. Bayes to the new SeqDir
# create Mr. Bayes driver
if not os.path.exists(seq_dir + tree + "\\" + tree + "-command.nex"):
outfile = open(seq_tree_dir + tree + "-command.nex",'w')
outfile.write("#NEXUS\n")
outfile.write("\n")
outfile.write("begin mrbayes;\n")
outfile.write("\t" + "set autoclose=yes nowarn=yes;\n")
outfile.write("\t" + "execute " + tree + ".nex;\n")
outfile.write("\t" + "lset nst=6 rates=invgamma;\n")
