def test_dn_ds(self):
from Bio.codonalign.codonseq import cal_dn_ds
codon_seq1 = self.aln[0]
codon_seq2 = self.aln[1]
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='NG86')
self.assertAlmostEqual(round(dN, 4), 0.0209, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0178, places=4)
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='LWL85')
self.assertAlmostEqual(round(dN, 4), 0.0203, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0164, places=4)
try:
import scipy
except ImportError:
# Silently skip the rest of the test
return
# This should be present:
from scipy.linalg import expm
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='YN00')
self.assertAlmostEqual(round(dN, 4), 0.0198, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0222, places=4)
try:
# New in scipy v0.11
from scipy.optimize import minimize
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='ML')
self.assertAlmostEqual(round(dN, 4), 0.0194, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0217, places=4)
except ImportError:
# TODO - Show a warning?
pass
def test_dn_ds(self):
from Bio.codonalign.codonseq import cal_dn_ds
codon_seq1 = self.aln[0]
codon_seq2 = self.aln[1]
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='NG86')
self.assertAlmostEqual(round(dN, 4), 0.0209, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0178, places=4)
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='LWL85')
self.assertAlmostEqual(round(dN, 4), 0.0203, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0164, places=4)
try:
import scipy
except ImportError:
# Silently skip the rest of the test
return
# This should be present:
from scipy.linalg import expm
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='YN00')
self.assertAlmostEqual(round(dN, 4), 0.0198, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0222, places=4)
try:
# New in scipy v0.11
from scipy.optimize import minimize
dN, dS = cal_dn_ds(codon_seq1, codon_seq2, method='ML')
self.assertAlmostEqual(round(dN, 4), 0.0194, places=4)
self.assertAlmostEqual(round(dS, 4), 0.0217, places=4)
except ImportError:
# TODO - Show a warning?
pass
def calculate_piN_piS(codonseqs, method, codon_table, het=False):
"""
takes a list of CodonSeq() objects and calculates piN, piS, pi, and piNpiS
for them
"""
analysis = {
"seqname": "",
"piN": -1,
"piS": -1,
"piNpiS": -1,
"pi": -1,
"method": method
}
x = seqfreqs(codonseqs)
#if 'piNpiS' in options.debug:
# print("freqs are: {}".format(x))
# print("len codonseqs is: ", len(codonseqs))
piN = 0
piS = 0
for i in range(len(codonseqs)):
for j in range(i + 1, len(codonseqs)):
#print(codonseqs[i], codonseqs[j])
if not het:
dN, dS = cal_dn_ds(codonseqs[i],
codonseqs[j],
codon_table=codon_table,
method=method)
piN = piN + (x[i] * x[j] * dN)
piS = piS + (x[i] * x[j] * dS)
#if 'piNpiS' in options.debug:
# print("{0} dN{1}{2}={3} dS{1}{2}={4}".format(method, i, j, dN, dS))
else:
try:
dN, dS = cal_dn_ds(codonseqs[i],
codonseqs[j],
codon_table=codon_table,
method=method)
piN = piN + (x[i] * x[j] * dN)
piS = piS + (x[i] * x[j] * dS)
except:
pass
analysis['piN'] = piN
analysis['piS'] = piS
try:
analysis['piNpiS'] = piN / piS
except:
analysis['piNpiS'] = 0
#if 'piNpiS' in options.debug:
# print ("{0} dN={1:.3f} dS={2:.3f} piN/piS = {3:.3f}".format(
# method, analysis['piN'], analysis['piS'], analysis['piNpiS']))
return analysis
def get_dn_ds_matrix(self, method="NG86", codon_table=default_codon_table):
"""Available methods include NG86, LWL85, YN00 and ML.
Argument:
- method - Available methods include NG86, LWL85, YN00 and ML.
- codon_table - Codon table to use for forward translation.
"""
from Bio.Phylo.TreeConstruction import _DistanceMatrix as DM
names = [i.id for i in self._records]
size = len(self._records)
dn_matrix = []
ds_matrix = []
for i in range(size):
dn_matrix.append([])
ds_matrix.append([])
for j in range(i + 1):
if i != j:
dn, ds = cal_dn_ds(self._records[i],
self._records[j],
method=method,
codon_table=codon_table)
dn_matrix[i].append(dn)
ds_matrix[i].append(ds)
else:
dn_matrix[i].append(0.0)
ds_matrix[i].append(0.0)
dn_dm = DM(names, matrix=dn_matrix)
ds_dm = DM(names, matrix=ds_matrix)
return dn_dm, ds_dm
def get_dn_ds_matrix(self, method="NG86", codon_table=default_codon_table):
"""Available methods include NG86, LWL85, YN00 and ML.
Argument:
- method - Available methods include NG86, LWL85, YN00 and ML.
- codon_table - Codon table to use for forward translation.
"""
from Bio.Phylo.TreeConstruction import _DistanceMatrix as DM
names = [i.id for i in self._records]
size = len(self._records)
dn_matrix = []
ds_matrix = []
for i in range(size):
dn_matrix.append([])
ds_matrix.append([])
for j in range(i + 1):
if i != j:
dn, ds = cal_dn_ds(self._records[i], self._records[j], method=method, codon_table=codon_table)
dn_matrix[i].append(dn)
ds_matrix[i].append(ds)
else:
dn_matrix[i].append(0.0)
ds_matrix[i].append(0.0)
dn_dm = DM(names, matrix=dn_matrix)
ds_dm = DM(names, matrix=ds_matrix)
return dn_dm, ds_dm
def get_dn_ds_matrix(self, method="NG86"):
"""Available methods include NG86, LWL85, YN00 and ML.
"""
from Bio.Phylo.TreeConstruction import _DistanceMatrix as DM
names = [i.id for i in self._records]
size = len(self._records)
dn_matrix = []
ds_matrix = []
for i in range(size):
dn_matrix.append([])
ds_matrix.append([])
for j in range(i + 1):
if i != j:
dn, ds = cal_dn_ds(self._records[i], self._records[j],
method=method)
dn_matrix[i].append(dn)
ds_matrix[i].append(ds)
else:
dn_matrix[i].append(0.0)
ds_matrix[i].append(0.0)
dn_dm = DM(names, matrix=dn_matrix)
ds_dm = DM(names, matrix=ds_matrix)
return dn_dm, ds_dm
def divergence():
########################
## Arguments d'entrée ##
########################
fic1dna = sys.argv[1] #fichier des séquences adn de l'espèce 1
fic2dna = sys.argv[2] #fichier des séquences adn de l'espèce 2
fic1prot = sys.argv[3] #fichier des séquences protéiques de l'espèce 1
fic2prot = sys.argv[4] #fichier des séquences protéiques de l'espèce 2
#outfile_unaligned="outfile_unaligned.fa"
#outfile_unaligned=open(outfile_unaligned,"w",encoding='utf-8')
outfile_dn_ds = sys.argv[5] #fichier de sortie format tableau, sep = ";"
outfile_dn_ds = open(outfile_dn_ds, "w", encoding='utf-8')
method = sys.argv[6] #Methode utilisée
muscle_exe = sys.argv[7] #Chemin vers le fichier executable de MUSCLE
#Transformation des séquences en format SeqIO
seq1dna = list(
SeqIO.parse(fic1dna, "fasta", alphabet=IUPAC.IUPACUnambiguousDNA()))
seq2dna = list(
SeqIO.parse(fic2dna, "fasta", alphabet=IUPAC.IUPACUnambiguousDNA()))
seq1prot = list(SeqIO.parse(fic1prot, "fasta", alphabet=IUPAC.protein))
seq2prot = list(SeqIO.parse(fic2prot, "fasta", alphabet=IUPAC.protein))
#Première ligne du tableau "titres"
"""print("seq.id",";","dN",";","dS",";","Dist_third_pos",";","Dist_brute",";","Length_seq_1",";","Length_seq2",
";","GC_content_seq1",";","GC_content_seq2",";","GC",";","Mean_length",file=outfile_dn_ds)"""
print("Nombre de paires de sequences a analyser: ", len(seq1dna))
print("seq.id", ";", "dN", ";", "dS", ";", "Dist_third_pos", ";",
"Dist_brute", ";", "Length_seq_1", ";", "Length_seq2", ";",
"GC_content_seq1", ";", "GC_content_seq2", ";", "GC", ";",
"Mean_length")
"""df2 = pd.DataFrame(columns=("seq.id","dN","dS","Dist_third_pos","Dist_brute","Length_seq_1","Length_seq2",
"GC_content_seq1","GC_content_seq2","GC","Mean_length"))"""
#Boucle sur chaque paire de séquence
u = 0
while u < (len(seq1dna)):
try:
###########################################################
#. Alignement entre chaque paire de séquence #
###########################################################
nuc1 = str(seq1dna[u].seq
) #Récupère la séquence u et la transforme en string
nuc2 = str(seq2dna[u].seq)
prot1 = str(seq1prot[u].seq)
prot2 = str(seq2prot[u].seq)
protein2 = SeqRecord(
Seq(prot2, alphabet=IUPAC.protein), id='protein2'
) #Transformation de la séquence protéique en format SeqRecord
protein1 = SeqRecord(Seq(prot1, alphabet=IUPAC.protein),
id='protein1')
with open(
"outfile_unaligned.fa", "w", encoding='utf-8'
) as output_handle: #Permet de créer un fichier de deux séquences non-alignées (format fasta)
SeqIO.write(protein1, output_handle, "fasta")
SeqIO.write(protein2, output_handle, "fasta")
muscle_cline = MuscleCommandline(
muscle_exe,
input="outfile_unaligned.fa",
out="outfile_aligned.aln"
) #Prend en entrée le fichier de séquences non-alignées et sort un fichier de séquences alignées
stdout, stderr = muscle_cline()
alns = AlignIO.read(
"outfile_aligned.aln",
"fasta") #Lecture du fichier de séquences alignées
prot1 = str(alns[0].seq) #Récupère la séquence protéique 1 alignée
prot2 = str(alns[1].seq) #Récup§re la séquence protéique 2 alignée
nuc2 = SeqRecord(
Seq(nuc2, alphabet=IUPAC.IUPACUnambiguousDNA()), id='nuc2'
) #Transformation de la séquence nucléique en format SeqRecord
nuc1 = SeqRecord(Seq(nuc1, alphabet=IUPAC.IUPACUnambiguousDNA()),
id='nuc1')
prot1 = SeqRecord(
Seq(prot1, alphabet=IUPAC.protein), id='pro1'
) #Transformation de la séquence protéique en format SeqRecord
prot2 = SeqRecord(Seq(prot2, alphabet=IUPAC.protein), id='pro2')
aln = MultipleSeqAlignment(
[prot1, prot2]
) #Créer format alignement des 2 séquences protéiques préalablement alignées
codon_aln = codonalign.build(
aln, [nuc1, nuc2]) #Créer un alignement de codon
#Fichier d'alignement
#AlignIO.write(codon_aln,"outfile_aligned", 'fasta')
lengthseq1 = len(nuc1.seq)
lengthseq2 = len(nuc2.seq)
GCcontentseq1 = GC(nuc1.seq)
GCcontentseq2 = GC(nuc2.seq)
GC_mean = ((GCcontentseq1 + GCcontentseq2) / 2)
if lengthseq1 >= lengthseq2:
Min_length = lengthseq2
if lengthseq1 < lengthseq2:
Min_length = lengthseq1
##########################################################
# CALCULS DES INDICES DE DIVERGENCE #
##########################################################
#Calcul de divergence synonyme et non-synonyme
#Supression des gaps
seq1 = ""
seq2 = ""
for x, z in zip(codon_aln[0], codon_aln[1]):
if z == "-":
continue
if x == "-":
continue
else:
seq1 += x
seq2 += z
#################################################################
#. Comptage du nombre de site polymorhe brute #
#################################################################
#Compteur de différences par site
compteur0 = 0
for i, e in zip(seq1, seq2):
if i != e:
compteur0 += 1
distance_brute = round(float((compteur0) / len(seq1)), 3)
seq1_third_pos = ""
seq2_third_pos = ""
compteur1 = 0
for i in seq1[2::3]:
if i.isalpha():
seq1_third_pos += i
compteur1 += 1
compteur2 = 0
for i in seq2[2::3]:
if i.isalpha():
seq2_third_pos += i
compteur2 += 1
####################################################################
# Comptage du nombre de site polymorphe en troisième position #
####################################################################
#Compteur de différences par site (3ieme position)
compteur3 = 0
for i, e in zip(seq1_third_pos, seq2_third_pos):
if i != e:
compteur3 += 1
distance_third_pos = round(float((compteur3) / compteur2), 3)
####################################################################
# Calcul dN et dS selon la méthode utilisée #
####################################################################
try:
dN, dS = cal_dn_ds(codon_aln[0], codon_aln[1], method=method)
"""print(seq1dna[u].id,";",dN,";",dS,";",distance_third_pos,";",distance_brute,";",lengthseq1,
";",lengthseq2,";",GCcontentseq1,";",GCcontentseq2,";",GC_mean,";",Min_length,file=outfile_dn_ds)"""
print(seq1dna[u].id, ";", dN, ";", dS, ";", distance_third_pos,
";", distance_brute, ";", lengthseq1, ";", lengthseq2,
";", GCcontentseq1, ";", GCcontentseq2, ";", GC_mean,
";", Min_length)
"""df2=df2.append({"seq.id":seq1dna[u].id,"dN":dN,"dS":dS,"Dist_third_pos":distance_third_pos,"Dist_brute":distance_brute,"Length_seq_1":lengthseq1,
"Length_seq2":lengthseq2,"GC_content_seq1":GCcontentseq1,"GC_content_seq2":GCcontentseq2,"GC":GC_mean,"Mean_length":Min_length}, ignore_index=True)"""
except ValueError:
result = 9.999 #Saturation trop importante pour calculer les indices.
"""print(seq1dna[u].id,";",result,";",result,";",distance_third_pos,";",distance_brute,";",lengthseq1,
";",lengthseq2,";",GCcontentseq1,";",GCcontentseq2,";",GC_mean,";",Min_length,file=outfile_dn_ds)"""
print(seq1dna[u].id, ";", result, ";", result, ";",
distance_third_pos, ";", distance_brute, ";", lengthseq1,
";", lengthseq2, ";", GCcontentseq1, ";", GCcontentseq2,
";", GC_mean, ";", Min_length)
"""df2=df2.append({"seq.id":seq1dna[u].id,"dN":result,"dS":result,"Dist_third_pos":distance_third_pos,"Dist_brute":distance_brute,"Length_seq_1":lengthseq1,
"Length_seq2":lengthseq2,"GC_content_seq1":GCcontentseq1,"GC_content_seq2":GCcontentseq2,"GC":GC_mean,"Mean_length":Min_length}, ignore_index=True)"""
except ZeroDivisionError:
result = 9.999
"""print(seq1dna[u].id,";",result,";",result,";",distance_third_pos,";",distance_brute,";",lengthseq1,
";",lengthseq2,";",GCcontentseq1,";",GCcontentseq2,";",GC_mean,";",Min_length,file=outfile_dn_ds)"""
print(seq1dna[u].id, ";", result, ";", result, ";",
distance_third_pos, ";", distance_brute, ";", lengthseq1,
";", lengthseq2, ";", GCcontentseq1, ";", GCcontentseq2,
";", GC_mean, ";", Min_length)
"""df2=df2.append({"seq.id":seq1dna[u].id,"dN":result,"dS":result,"Dist_third_pos":distance_third_pos,"Dist_brute":distance_brute,"Length_seq_1":lengthseq1,
"Length_seq2":lengthseq2,"GC_content_seq1":GCcontentseq1,"GC_content_seq2":GCcontentseq2,"GC":GC_mean,"Mean_length":Min_length}, ignore_index=True)"""
except KeyError:
result = 9.999
"""print(seq1dna[u].id,";",result,";",result,";",distance_third_pos,";",distance_brute,";",lengthseq1,
";",lengthseq2,";",GCcontentseq1,";",GCcontentseq2,";",GC_mean,";",Min_length,file=outfile_dn_ds)"""
print(seq1dna[u].id, ";", result, ";", result, ";",
distance_third_pos, ";", distance_brute, ";", lengthseq1,
";", lengthseq2, ";", GCcontentseq1, ";", GCcontentseq2,
";", GC_mean, ";", Min_length)
"""df2=df2.append({"seq.id":seq1dna[u].id,"dN":result,"dS":result,"Dist_third_pos":distance_third_pos,"Dist_brute":distance_brute,"Length_seq_1":lengthseq1,
"Length_seq2":lengthseq2,"GC_content_seq1":GCcontentseq1,"GC_content_seq2":GCcontentseq2,"GC":GC_mean,"Mean_length":Min_length}, ignore_index=True)"""
u += 1
except:
traceback.print_exc()
print("Une erreur est survenue pour la sequence: ", seq1dna[u].id,
"vs", seq2dna[u].id)
"""df2=df2.append({"seq.id":seq1dna[u].id,"dN":"NA","dS":"NA","Dist_third_pos":"NA","Dist_brute":"NA","Length_seq_1":"NA",
"Length_seq2":"NA","GC_content_seq1":"NA","GC_content_seq2":"NA","GC":"NA","Mean_length":"NA"}, ignore_index=True)"""
u += 1
#df2.to_csv(outfile_dn_ds, sep='\t')
outfile_dn_ds.close() #Fermeture du fichier ouvert
index_Cap = int([names.index(i) for i in names if 'Capybara' in i][0])
index_Cpor = int([names.index(i) for i in names if 'Cavia' in i][0])
CapCDS = aln.takeSeqs([names[index_Cap]])
Cap_seqs.append(CapCDS.getSeqNames()[0].split('|')[1])
CporCDS = aln.takeSeqs([names[index_Cpor]])
Cpor_seqs.append(CporCDS.getSeqNames()[0].split('|')[1])
if ((len(aln) / len(aln1)) > 0.5):
#Solo analizar alineaientos que despues de eliminados los gaps, tengan una longitud mayor al 50% de la longitud original
CapCDSstr = str(CapCDS.todict().values()[0])
CapCDSstr = str(CapCDS.todict().values()[0])
CapCDSstr = CodonSeq(CapCDSstr)
CporCDSstr = str(CporCDS.todict().values()[0])
CporCDSstr = CodonSeq(CporCDSstr)
try:
if cal_dn_ds(CapCDSstr, CporCDSstr)[1] == 0.0:
val1 = 0.0
else:
val1 = cal_dn_ds(CapCDSstr, CporCDSstr)[0] / cal_dn_ds(
CapCDSstr, CporCDSstr)[1]
CGP.append(val1)
except:
print 'Error with: ' + os.path.split(
sequences[s])[-1].split('_')[0]
else:
CGP.append('NA')
#s = s + 1
Cpor_seqs = np.array(Cpor_seqs)
Cap_seqs = np.array(Cap_seqs)
CGP = np.array(CGP)
Cap_seqs.append(CapCDS.getSeqNames()[0].split('|')[1])
CporCDS = aln.takeSeqs([names[index_Cpor]])
Cpor_seqs.append(CporCDS.getSeqNames()[0].split('|')[1])
RatCDS = aln.takeSeqs([names[index_Rat]])
Rat_seqs.append(RatCDS.getSeqNames()[0])
if ((len(aln) / len(aln1)) > 0.5):
#Solo analizar alineaientos que despues de eliminados los gaps, tengan una longitud mayor al 50% de la longitud original
CapCDSstr = str(CapCDS.todict().values()[0])
CapCDSstr = CodonSeq(CapCDSstr)
CporCDSstr = str(CporCDS.todict().values()[0])
CporCDSstr = CodonSeq(CporCDSstr)
RatCDSstr = str(RatCDS.todict().values()[0])
RatCDSstr = CodonSeq(RatCDSstr)
try:
if cal_dn_ds(CapCDSstr, CporCDSstr)[1] == 0.0:
val1 = 0.0
elif cal_dn_ds(CporCDSstr, RatCDSstr)[1] == 0.0:
val2 = 0.0
else:
val1 = cal_dn_ds(CapCDSstr, CporCDSstr)[0] / cal_dn_ds(
CapCDSstr, CporCDSstr)[1]
val2 = cal_dn_ds(CporCDSstr, RatCDSstr)[0] / cal_dn_ds(
CporCDSstr, RatCDSstr)[1]
CGP.append(val1)
GPR.append(val2)
except:
print 'Error with: ' + os.path.split(
sequences[s])[-1].split('_')[0]
else:
CGP.append('NA')