def testParseAllVersions(self):
pattern = os.path.join(self.results_dir, "yn00", "yn00-*")
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
self.assertEqual(len(results), 5)
self.assertEqual(len(results["Homo_sapie"]), 4)
self.assertEqual(len(results["Homo_sapie"]["Pan_troglo"]), 5)
def testParseAllVersions(self):
pattern = os.path.join(self.results_dir, "yn00", 'yn00-*')
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
self.assertEqual(len(results), 5)
self.assertEqual(len(results["Homo_sapie"]), 4)
self.assertEqual(len(results["Homo_sapie"]["Pan_troglo"]), 5)
def testParseAllVersions(self):
folder = os.path.join(self.results_dir, "yn00")
for results_file in os.listdir(folder):
file_path = os.path.join(folder, results_file)
results = yn00.read(file_path)
self.assertEqual(len(results), 5)
self.assertEqual(len(results["Homo_sapie"]), 4)
self.assertEqual(len(results["Homo_sapie"]["Pan_troglo"]), 5)
def testParseAllVersions(self):
folder = os.path.join(self.results_dir, "yn00")
for results_file in os.listdir(folder):
file_path = os.path.join(folder, results_file)
results = yn00.read(file_path)
self.assertEqual(len(results), 5)
self.assertEqual(len(results["Homo_sapie"]), 4)
self.assertEqual(len(results["Homo_sapie"]["Pan_troglo"]),
5)
def testParseAllVersions(self):
folder = os.path.join("PAML", "Results", "yn00", "versions")
for results_file in os.listdir(folder):
file_path = os.path.join(folder, results_file)
if os.path.isfile(file_path) and results_file[:4] == "yn00":
results = yn00.read(file_path)
self.assertEqual(len(results), 5)
self.assertEqual(len(results["Homo_sapie"]), 4)
self.assertEqual(len(results["Homo_sapie"]["Pan_troglo"]), 5)
def testParseLongNames(self):
pattern = os.path.join(self.results_dir, "yn00", 'yn00_long-*')
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
# Expect seven taxa...
self.assertEqual(len(results), 7)
# ...each of which is compared to the other six.
self.assertEqual(set([len(v) for v in results.values()]), set([6]))
# ...each of which has five measures.
self.assertEqual(set([len(v) for taxa in results.values() for v in taxa.values()]), set([5]))
def testParseAllVersions(self):
folder = os.path.join("PAML","Results", "yn00", "versions")
for results_file in os.listdir(folder):
file_path = os.path.join(folder, results_file)
if os.path.isfile(file_path) and results_file[:4] == "yn00":
results = yn00.read(file_path)
self.assertEqual(len(results), 5)
self.assertEqual(len(results["Homo_sapie"]), 4)
self.assertEqual(len(results["Homo_sapie"]["Pan_troglo"]),
5)
def testParseLongNames(self):
pattern = os.path.join(self.results_dir, "yn00", 'yn00_long-*')
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
# Expect seven taxa...
self.assertEqual(len(results), 7)
# ...each of which is compared to the other six.
self.assertEqual(set([len(v) for v in results.values()]), set([6]))
# ...each of which has five measures.
self.assertEqual(set([len(v) for taxa in results.values() for v in taxa.values()]), set([5]))
def testParseDottedNumNames(self):
pattern = os.path.join(self.results_dir, "yn00", 'yn00_dottednum-*')
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
# Expect seven taxa...
self.assertEqual(len(results), 7)
# ...each of which is compared to the other six.
self.assertEqual({len(v) for v in results.values()}, {6})
# ...each of which has five measures.
self.assertEqual({len(v) for taxa in results.values() for v in taxa.values()}, {5})
def SummarizeYn00(refine=False):
"""
Summarize yn00 results for core and accessory gene clusters and write to file.
"""
results = {}
if refine:
clusters = glob(
"./panoct/clusters/refined/core/fna/Core*.fna.aln.yn00") + glob(
"./panoct/clusters/refined/acc/fna/Acc*.fna.aln.yn00")
else:
clusters = glob("./panoct/clusters/core/fna/Core*.fna.aln.yn00"
) + glob("./panoct/clusters/acc/fna/Acc*.fna.aln.yn00")
for cluster in clusters:
cl_number = cluster.split("_")[1].split(".")[0]
cl_comp = cluster.split("_")[0].split("/")[-1]
results[cl_number] = {
"Component": cl_comp,
"Size": None,
"Kappa": None,
"Omega > 1": None
}
try:
yn = yn00.read(cluster)
results[cl_number]["Size"] = len(yn)
if len(yn) == 1:
pass
else:
with_omega = 0
for gene in yn:
for subject in yn[gene]:
pair = yn[gene][subject]["YN00"]
if not results[cl_number]["Kappa"]:
results[cl_number]["Kappa"] = pair["kappa"]
if all([pair["dS"] == -0.0, pair["omega"] == 99.0]):
pass
elif pair["omega"] > 1.0:
with_omega = with_omega + 1
results[cl_number]["Omega > 1"] = with_omega / 2
except (IndexError, ValueError):
pass
with open("./panoct/clusters/yn00_summary.txt", "w") as output:
output.write("Cluster\tComponent\tSize\tKappa\tOmega > 1\n")
for cluster in results:
output.write("{0}\t{1}\t{2}\t{3}\t{4}\n".format(
str(cluster), results[cluster]["Component"],
results[cluster]["Size"], results[cluster]["Kappa"],
results[cluster]["Omega > 1"]))
to_remove = ["rub", "rst1", "rst", "yn00.ctl", "2YN.dS", "2YN.dN", "2YN.t"]
for f in to_remove:
if os.path.isfile(f):
os.remove(f)
def testParseDottedNames(self):
pattern = os.path.join(self.results_dir, "yn00", 'yn00_dotted-*')
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
# Expect seven taxa...
self.assertEqual(len(results), 5)
# ...each of which is compared to the other six.
self.assertEqual(set([len(v) for v in results.values()]), set([4]))
# ...each of which has five measures.
self.assertEqual(set([len(v) for taxa in results.values() for v in taxa.values()]), set([5]))
self.assertEqual(len(results["H**o.sapie"]), 4)
self.assertEqual(len(results["H**o.sapie"]["Pan.troglo"]), 5)
def testParseDottedNames(self):
pattern = os.path.join(self.results_dir, "yn00", "yn00_dotted-*")
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
# Expect seven taxa...
self.assertEqual(len(results), 5)
# ...each of which is compared to the other six.
self.assertEqual({len(v) for v in results.values()}, {4})
# ...each of which has five measures.
self.assertEqual(
{len(v)
for taxa in results.values() for v in taxa.values()}, {5})
self.assertEqual(len(results["H**o.sapie"]), 4)
self.assertEqual(len(results["H**o.sapie"]["Pan.troglo"]), 5)
import os
from sys import argv
from Bio.Phylo.PAML import yn00
script, folder = argv
folder_in = os.listdir(folder)
oup = open("pairwise_dNdS.txt", "w")
oup.write("file\tpair\tdNdS\tdN\tdS\n")
for inl in folder_in:
print inl
result = yn00.read("%s/%s" % (folder, inl))
for k in result.keys():
if "BSIN" in k:
dNx = dSx = Wx = 0
for x in result[k].keys():
if "WS68" in x:
dNx = result[k][x]["YN00"]["dN"]
dSx = result[k][x]["YN00"]["dS"]
Wx = result[k][x]["YN00"]["omega"]
oup.write("%s\tBSIN_WS68\t%r\t%r\t%r\n" %
(inl, Wx, dNx, dSx))
else:
pass
elif "AQ15" in k:
dNy = dSy = Wy = 0
for x in result[k].keys():
if taxons[organism] in i:
copy1 = i.replace(taxons[organism], "")
copy2 = inparalogs_dic[i].replace(taxons[organism], "")
if copy1 in organism_fasta and copy2 in organism_fasta:
seq1 = organism_fasta[copy1]
seq2 = organism_fasta[copy2]
namealnphy = copy1 + "_" + copy2 + ".aln.phy"
print("Runing yn00 for", namealnphy)
#run PAML yn00 software
yn = yn00.Yn00()
yn.alignment = namealnphy
yn.out_file = "yn_out.txt"
yn.working_dir = "./"
yn.commonf3x4 = 1
yn.weighting = None
yn.icode = None
yn.ndata = None
yn.verbose = None
yn.run()
result = yn00.read("yn_out.txt")[copy1]
for uu in result.values():
ds = str(uu["YN00"]["dS"])
dsse = str(uu["YN00"]["dS SE"])
dn = str(uu["YN00"]["dN"])
dnse = str(uu["YN00"]["dN SE"])
output_yn00.write(copy1 + "\t" + copy2 + "\t" + ds + "\t" +
dsse + "\t" + dn + "\t" + dnse + "\n")
os.remove(namealnphy)
