infile = args.infile
mapfile = args.map
outgroup = args.outgroup
triples = parse_triples(args.triples)
nind = args.num_ind
ntaxa = args.num_taxa
nsites = args.num_sites
threads = args.threads
prefix = args.prefix
quiet = args.quiet
ignore_amb_sites = args.ignore_amb_sites
if not quiet: print("\nRunning individual_hyde_mp.py")
# Read data into a HydeData object
data = hd.HydeData(infile, mapfile, outgroup, nind, ntaxa, nsites, quiet,
ignore_amb_sites)
if not quiet:
print("\nAnalyzing",
len(triples),
"triple(s) using",
threads,
"thread(s).",
sep=' ')
outpath = hd.expand_prefix(prefix)
if os.path.exists(outpath + "-ind.txt"):
if not quiet:
print("\n** Warning: File '" + outpath +
"-ind.txt' already exists. **")
if not quiet:
help="supress printing to stdout")
args = parser.parse_args()
infile = args.infile
mapfile = args.map
outgroup = args.outgroup
triples = parse_triples(args.triples)
nind = args.num_ind
ntaxa = args.num_taxa
nsites = args.num_sites
prefix = args.prefix
quiet = args.quiet
if not quiet: print("\nRunning individual_hyde.py")
data = hd.HydeData(infile, mapfile, outgroup, nind, ntaxa, nsites, quiet)
# Read data into a HydeData object
if not quiet:
print("\nAnalyzing", len(triples), "triple(s).", sep=' ')
outpath = hd.expand_prefix(prefix)
if os.path.exists(outpath + "-ind.txt"):
if not quiet:
print("\n** Warning: File '" + outpath +
"-ind.txt' already exists. **")
if not quiet:
print("** Renaming to '" + outpath + "-ind-old.txt'. **\n")
os.rename(outpath + "-ind.txt", outpath + "-ind-old.txt")
outfile = open(outpath + "-ind.txt", 'a')
else:
# get partial paths of every phylip input file in paths (these end in seqgen.out)
phylip_paths = []
numTrees = ["knownGT/n10/seqgen/", "knownGT/n15/seqgen/", "n25h5/", "n50h10/", "n100h25/"]
for tree_nums in numTrees:
for subfolder in os.listdir(input_path + tree_nums):
try:
for f in os.listdir(input_path + tree_nums + subfolder):
if ".phylip" in f:
phylip_paths.append(tree_nums + subfolder + "/" + f)
except OSError:
print("") # do nothing
# the top of the phylip files should have the number of taxa and number of sites:
# note that hyde documentation says that "it is typically difficult to detect hybridization
# using less than 10,000 sites"
print("hello")
for file in phylip_paths:
# create mapfile?
num_taxa =
num_sites =
num_individuals = num_taxa # ?
print("dat1")
dat = hd.HydeData(file, file, "10", 10, 10, 500)
print("dat")
#!/usr/bin/env python
from __future__ import print_function
import phyde as hd
print("HyDe version: ", hd.__version__, sep='')
print("\n**** Test 1: Data import. ****")
data = hd.HydeData("data.txt", "map.txt", "out", 16, 4, 50000)
print("**** Good. ****")
print("\n**** Test 2: Running test_triple(). ****")
print(data.test_triple('sp1', 'sp2', 'sp3'))
print("**** Good. ****")
print("\n**** Test 3: Running test_individuals(). ****")
print(data.test_individuals('sp1', 'sp2', 'sp3'))
print("**** Good. ****")
print("\n**** Test 4: Running bootstrap_triple(). ****")
print(data.bootstrap_triple('sp1', 'sp2', 'sp3', 20))
print("**** Good. ****")
print("\n**** Test 5: Reading in HyDe results. ****")
res2 = hd.HydeResult("../hyde-out.txt")
print("**** Good. ****")
print("\n**** Test 6: Testing ABBA-BABA on HydeResult object. ****")
print(res2.abba_baba("sp1", "sp2", "sp3"))
print("**** Good. ****")
