def calculIdenticNeedleCross(l_p_fasta, pr_alignement):
"""
Calcul identity structure
args: -> list of fasta files
return: -> dictionary with identity
"""
if len(l_p_fasta) == 1:
return []
dico_out = {}
if len(l_p_fasta) == 2:
first_key = l_p_fasta[0].split("/")[-1][0:-6]
dico_out[first_key] = {}
if not path.exists(pr_alignement + first_key + "_" +
l_p_fasta[1].split("/")[-1][0:-6] + ".needle"):
path_file_needle = runOtherSoft.needle(
l_p_fasta[0], l_p_fasta[1], pr_alignement + first_key + "_" +
l_p_fasta[1].split("/")[-1][0:-6] + ".needle")
else:
path_file_needle = pr_alignement + first_key + "_" + l_p_fasta[
1].split("/")[-1][0:-6] + ".needle"
dico_out[first_key][l_p_fasta[1].split(
"/")[-1][0:-6]] = parseEMBOSS.embossFile(path_file_needle)[3]
else:
nb_fasta = len(l_p_fasta)
i = 0
while i < nb_fasta - 1:
first_key = l_p_fasta[i].split("/")[-1][0:-6]
dico_out[first_key] = {}
j = i + 1
while j < nb_fasta:
if not path.exists(pr_alignement + first_key + "_" +
l_p_fasta[j].split("/")[-1][0:-6] +
".needle"):
path_file_needle = runOtherSoft.needle(
l_p_fasta[i], l_p_fasta[j], pr_alignement + first_key +
"_" + l_p_fasta[j].split("/")[-1][0:-6] + ".needle")
if path.exists(pr_alignement + first_key + "_" +
l_p_fasta[j].split("/")[-1][0:-6] +
".needle"): # case DNA sequence in fasta
dico_out[first_key][l_p_fasta[j].split(
"/")[-1][0:-6]] = parseEMBOSS.embossFile(
pr_alignement + first_key + "_" +
l_p_fasta[j].split("/")[-1][0:-6] + ".needle")[3]
j = j + 1
i = i + 1
# for i in dico_out.keys () :
# print dico_out[i]
return dico_out
def calculIdenticNeedleCross(l_p_fasta, pr_alignement) :
"""
Calcul identity structure
args: -> list of fasta files
return: -> dictionary with identity
"""
if len (l_p_fasta) == 1 :
return []
dico_out = {}
if len (l_p_fasta) == 2 :
first_key = l_p_fasta[0].split("/")[-1][0:-6]
dico_out[first_key] = {}
if not path.exists( pr_alignement + first_key + "_" + l_p_fasta[1].split("/")[-1][0:-6] + ".needle") :
path_file_needle = runOtherSoft.needle(l_p_fasta[0], l_p_fasta[1], pr_alignement + first_key + "_" + l_p_fasta[1].split("/")[-1][0:-6] + ".needle")
else :
path_file_needle = pr_alignement + first_key + "_" + l_p_fasta[1].split("/")[-1][0:-6] + ".needle"
dico_out[first_key] [l_p_fasta[1].split("/")[-1][0:-6]] = parseEMBOSS.embossFile(path_file_needle)[3]
else :
nb_fasta = len (l_p_fasta)
i = 0
while i < nb_fasta-1 :
first_key = l_p_fasta[i].split("/")[-1][0:-6]
dico_out[first_key] = {}
j = i + 1
while j < nb_fasta :
if not path.exists( pr_alignement + first_key + "_" + l_p_fasta[j].split("/")[-1][0:-6] + ".needle") :
path_file_needle = runOtherSoft.needle(l_p_fasta[i], l_p_fasta[j], pr_alignement + first_key + "_" + l_p_fasta[j].split("/")[-1][0:-6] + ".needle")
if path.exists( pr_alignement + first_key + "_" + l_p_fasta[j].split("/")[-1][0:-6] + ".needle") : # case DNA sequence in fasta
dico_out[first_key] [l_p_fasta[j].split("/")[-1][0:-6]] = parseEMBOSS.embossFile(pr_alignement + first_key + "_" + l_p_fasta[j].split("/")[-1][0:-6] + ".needle")[3]
j = j + 1
i = i + 1
# for i in dico_out.keys () :
# print dico_out[i]
return dico_out
def applyNeedleList(l_file_fasta, pr_out):
nb_pr_ref = len(l_file_fasta)
d_out = {}
i = 0
while i < nb_pr_ref:
j = i + 1
PDB1 = l_file_fasta[i].split("/")[-1][0:4]
# print PDB1
while j < nb_pr_ref:
PDB2 = l_file_fasta[j].split("/")[-1][0:4]
# folder TM align
p_outfile = runOtherSoft.needle(
l_file_fasta[i], l_file_fasta[j],
pr_out + PDB1 + "__" + PDB2 + ".needle")
out = parseEMBOSS.embossFile(p_outfile)
# list 0-> seq1, 1-> seq2, 2-> similarity, 3->identity
# print out[2:]
# parse result
if not PDB1 in d_out.keys():
if not PDB2 in d_out.keys():
d_out[PDB1] = {}
d_out[PDB1][PDB2] = {}
d_out[PDB1][PDB2]["identity"] = out[3].replace("%", "")
d_out[PDB1][PDB2]["similarity"] = out[2].replace("%", "")
else:
d_out[PDB2][PDB1] = {}
d_out[PDB2][PDB1]["identity"] = out[3].replace("%", "")
d_out[PDB2][PDB1]["similarity"] = out[2].replace("%", "")
else:
d_out[PDB1][PDB2] = {}
d_out[PDB1][PDB2]["identity"] = out[3].replace("%", "")
d_out[PDB1][PDB2]["similarity"] = out[2].replace("%", "")
j = j + 1
i = i + 1
return d_out
def applyNeedleList (l_file_fasta, pr_out):
nb_pr_ref = len (l_file_fasta)
d_out = {}
i = 0
while i < nb_pr_ref :
j = i + 1
PDB1 = l_file_fasta[i].split ("/")[-1][0:4]
# print PDB1
while j < nb_pr_ref :
PDB2 = l_file_fasta[j].split ("/")[-1][0:4]
# folder TM align
p_outfile = runOtherSoft.needle (l_file_fasta[i], l_file_fasta[j], pr_out + PDB1 + "__" + PDB2 + ".needle")
out = parseEMBOSS.embossFile(p_outfile)
# list 0-> seq1, 1-> seq2, 2-> similarity, 3->identity
# print out[2:]
# parse result
if not PDB1 in d_out.keys () :
if not PDB2 in d_out.keys () :
d_out[PDB1] = {}
d_out[PDB1][PDB2] = {}
d_out[PDB1][PDB2]["identity"] = out[3].replace ("%", "")
d_out[PDB1][PDB2]["similarity"] = out[2].replace ("%", "")
else :
d_out[PDB2][PDB1] = {}
d_out[PDB2][PDB1]["identity"] = out[3].replace ("%", "")
d_out[PDB2][PDB1]["similarity"] = out[2].replace ("%", "")
else :
d_out[PDB1][PDB2] = {}
d_out[PDB1][PDB2]["identity"] = out[3].replace ("%", "")
d_out[PDB1][PDB2]["similarity"] = out[2].replace ("%", "")
j = j + 1
i = i + 1
return d_out
