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#!/usr/bin/python3
import sys
if len(sys.argv) !=2:
sys.stdout.write("Mandatory: python3 discoSnp_to_csv.py prefix_coherent_k_kval_c_cval.fa\n")
sys.stdout.write("This program formats the .fa to .csv format by puting each couple of .fa sequence (4 lines = 2 comments + 2 nucleotide sequences) into one line, replacing the '|' character by spaces and removing the CX_ formating")
sys.exit(1)
f=open(sys.argv[1], "r")
while 1:
com1_1=f.readline()
if not com1_1:
break
data1_1=f.readline()
if not data1_1:
break
com1_2=f.readline()
if not com1_2:
break
data1_2=f.readline()
if not data1_2:
break
com1_tab=com1_1.split("|")
# prints all before coverages
for i in range(0,4):
sys.stdout.write( com1_tab[i]+",")
# prints coverages
i=4
while com1_tab[i][0:1]!="C" and i<len(com1_tab):
i+=1
while com1_tab[i][0:1]=="C":
sys.stdout.write( com1_tab[i].split("_")[1]+",")
i+=1
# prints all remaining
while i<len(com1_tab)-1:
sys.stdout.write( com1_tab[i]+",")
i+=1
sys.stdout.write( com1_tab[i][:-1]+",")
sys.stdout.write(data1_1[:-1]+",")
com2_tab=com1_2.split("|")
# prints all before coverages
for i in range(0,4):
sys.stdout.write( com2_tab[i]+",")
# prints coverages
i=4
while com1_tab[i][0:1]!="C" and i<len(com1_tab):
i+=1
while com2_tab[i][0:1]=="C":
sys.stdout.write( com2_tab[i].split("_")[1]+",")
i+=1
# prints all remaining
while i<len(com2_tab)-1:
sys.stdout.write( com2_tab[i]+",")
i+=1
sys.stdout.write( com2_tab[i][:-1]+",")
print((data1_2,))
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