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#!/bin/python
# -*- coding: utf-8 -*-
###################################
# change extensions in uppercase and replace relative positions of SNPs in the header
# usage : keep_extensions_disco_file.py <disco_snps_file>.fa
import os
import sys
import getopt
import time
fichier = sys.argv[1]
output = sys.argv[2]
snp_file = open(fichier,"r")
snp_discobis = open(output, "w")
left_shift = 0
def findShift(line, mode):
headerComp = line.split("\n")[0].split("|")
left_shift = 0
prefix = 'left_unitig'
if mode == 1: prefix = 'left_contig'
for elt in headerComp:
if not elt.startswith(prefix): continue
left_shift = int(elt.split("_")[-1])
break
return left_shift
def replacePos(snp, left_shift):
new_pos = int(snp.split(":")[1].split("_")[0]) + left_shift
return snp.split(":")[0] + ":" + str(new_pos) + "_" + snp.split(":")[1].split("_")[1]
def replaceHeader(elt, left_shift):
if elt.startswith("P_"):
elt = ",".join([replacePos(snp, left_shift) for snp in elt.split(",")])
return elt
def contigOrUnitig():
#return 0 if unitig mode, 1 if contig mode
mode = 0
for line in snp_file:
headerComp = line.split("\n")[0].split("|")
for elt in headerComp:
if not elt.startswith("left_contig"): continue
mode = 1
break
return mode
mode = contigOrUnitig()
#back to the first line
snp_file.seek(0, 0)
for line in snp_file:
if not line.startswith(">"):
snp_discobis.write(line.upper())
continue
left_shift = findShift(line, mode)
if left_shift == 0:
snp_discobis.write(line)
continue
new_header = "|".join([replaceHeader(elt, left_shift) for elt in line.split("|")])
snp_discobis.write(ınew_header)
snp_file.close()
snp_discobis.close()
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