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09_OrganizeFolders_AND_run_SIXTET.py
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09_OrganizeFolders_AND_run_SIXTET.py
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#!/usr/bin/python
## Author: Eric FONTANILLAS
## Date: 06.12.12
## Object: Organize folder for run with the 6 species (Ap, Ac, Pp, Pg, Ps, Pf)
##################
###### DEF1 ######
##################
# Dans un multialignement fasta, cette fonction permet de formatter les noms de chaque sequence fasta dans le cas de COMPARAISON DE SEQUENCE PAR PAIR!!
def Get_SIXTET(F, number_sp):
list_locus = []
lists = []
list_SIXTET = F.readlines()
list_SIXTET = "".join(list_SIXTET)
list_SIXTET = list_SIXTET.split("\n")
del list_SIXTET[-1]
number = number_sp*2
i=0
j=0
m=0
z=0
while z < len(list_SIXTET) :
if list_SIXTET[z][0] == ">" :
list_SIXTET[z] = list_SIXTET[z].replace(list_SIXTET[z][0], "")
z+=1
while m < len(list_SIXTET)+2 :
i+=1
if i <= number :
list_locus.append(list_SIXTET[j])
else:
lists.append(list_locus)
list_locus = []
j = j-1
i=0
m+=1
j+=1
return(lists)
##############################################
###################
### RUN RUN RUN ###
###################
import string, os, zipfile, sys, re
## 1 ## Open input/output
## create a file with all loci
os.mkdir("./locus/")
zfile= zipfile.ZipFile(sys.argv[1])
for name in zfile.namelist() :
zfile.extract(name, "./locus/")
path_IN1 = "./locus/"
L_IN = os.listdir(path_IN1)
F1 = open("08_All_Loci_in_1_flat_file.fasta", "w")
for files in L_IN :
F0 = open("%s/%s" %(path_IN1,files), "r")
next = F0.readlines()
number_seq = 0
for seq in next :
number_seq += 1
F1.write(seq)
F0.close()
F1.close
number_sp = number_seq / 2 # number of species
os.system("rm -rf locus/")
F1 = open("08_All_Loci_in_1_flat_file.fasta", "r")
# create a file with a patron tree with the output of RAxML
i = 0
numbers = "[0-9]"
F3 = open("00_PATRON_TREE_FreeRatios.tree", "w")
F0 = open(sys.argv[2], "r")
next = F0.read()
next = next.split(":")
next = "".join(next)
while i<len(next) :
if re.match(numbers, next[i]) or re.match("\.", next[i]) :
next = next.replace(next[i], "")
i+=1
print next
F3.write(next)
F0.close
F3.close
F3 = open("00_PATRON_TREE_FreeRatios.tree", "r")
tree_patron_null = F3.read()
F3.close()
F3 = open("00_PATRON_TREE_FreeRatios.tree", "r")
tree_patron_alternate = F3.read()
F3.close()
os.mkdir("./TREE_FreeRatios")
path = "./TREE_FreeRatios"
## Read fasta file and split the multilocus file in several files
list_SIXTET = Get_SIXTET(F1, number_sp) ### DEF 1 ###
d = 1
for sixtet in list_SIXTET:
file_name = "locus_%d" %d
d = d+1
subpath_null = "%s/%s_NULL" %(path, file_name)
os.mkdir(subpath_null)
subpath_alternate = "%s/%s_ALTERNATE" %(path, file_name)
os.mkdir(subpath_alternate)
## copy codeml (from patron)
# NULL
os.system("cp 00_PATRON_codeml_NULL.ctl %s/codeml.ctl" %subpath_null)
# ALTERNATE
os.system("cp 00_PATRON_codeml_ALTERNATE.ctl %s/codeml.ctl" %subpath_alternate)
sixtet_fasta_null = open("%s/sixtet.fasta" %subpath_null, "w")
sixtet_fasta_alternate = open("%s/sixtet.fasta" %subpath_alternate, "w")
new_tree_patron_null = tree_patron_null
tree_file_null = open("%s/sixtet.tree" %subpath_null, "w")
new_tree_patron_alternate = tree_patron_alternate
tree_file_alternate = open("%s/sixtet.tree" %subpath_alternate, "w")
k = 0
n = k+1
while n<len(sixtet)+1 :
name = sixtet[k]
print name
short_name = name[0:2]
seq = sixtet[n]
ex1 = "(%s" %short_name
new_ex1 = "(%s" %name
ex2 = "%s)" %short_name
new_ex2 = "%s)" %name
new_tree_patron_null = new_tree_patron_null.replace(ex1, new_ex1, 1)
new_tree_patron_null = new_tree_patron_null.replace(ex2, new_ex2, 1)
new_tree_patron_alternate = new_tree_patron_alternate.replace(ex1, new_ex1, 1)
new_tree_patron_alternate = new_tree_patron_alternate.replace(ex2, new_ex2, 1)
sixtet_fasta_null.write(">%s\n" %name)
sixtet_fasta_null.write("%s\n" %seq)
sixtet_fasta_alternate.write(">%s\n" %name)
sixtet_fasta_alternate.write("%s\n" %seq)
k+=2
n+=2
sixtet_fasta_null.close()
sixtet_fasta_alternate.close()
tree_file_null.write(new_tree_patron_null)
tree_file_null.close()
tree_file_alternate.write(new_tree_patron_alternate)
tree_file_alternate.close()
## convert alignment file from fasta to phylip AND delete input fasta file
# NULL
CURRENT_PATH = os.path.abspath("./") ## Allow to go back to the script path
os.system("cp 00_PATRON_fasta2phylip.py %s/fasta2phylip.py" %subpath_null)
os.chdir("%s" %subpath_null)
os.system("./fasta2phylip.py")
os.system("codeml codeml.ctl") ## execute codeml
os.chdir(CURRENT_PATH)
# ALTERNATE
os.system("cp 00_PATRON_fasta2phylip.py %s/fasta2phylip.py" %subpath_alternate)
os.chdir("%s" %subpath_alternate)
os.system("./fasta2phylip.py")
os.system("codeml codeml.ctl") ## execute codeml
os.chdir(CURRENT_PATH)
F1.close()
F3.close()