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#!/usr/bin/python3
# -*- 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 sys
def contigOrUnitig(fa_file):
#return "unitig" or "contig"
mode = "unitig"
for line in fa_file:
headerComp = line.split("\n")[0].split("|")
for elt in headerComp:
if elt.startswith("left_contig"):
mode = "contig"
break
#back to the first line
fa_file.seek(0, 0)
return mode
def findShift(line, mode):
headerComp = line.split("\n")[0].split("|")
left_shift = 0
prefix = 'left_'+mode
for elt in headerComp:
if not elt.startswith(prefix): continue
left_shift = int(elt.split("_")[-1])
break
return left_shift
def replacePos(position, left_shift):
# SNP: P_1:30_C/T
# INDEL: P_1:30_2_11
new_pos = int(position.split(":")[1].split("_")[0]) + left_shift
res = position.split(":")[0] + ":" + str(new_pos)
for i in range (1,len(position.split(":")[1].split("_"))):
res += "_" + position.split(":")[1].split("_")[i]
return res
def replaceHeader(elt, left_shift):
if elt.startswith("P_"):
elt = ",".join([replacePos(position, left_shift) for position in elt.split(",")])
return elt
fa_file_name = sys.argv[1]
output_file_name = sys.argv[2]
fa_file = open(fa_file_name,"r")
fa_file_output = open(output_file_name, "w")
left_shift = 0
mode = contigOrUnitig(fa_file)
for line in fa_file:
if not line.startswith(">"):
fa_file_output.write(line.upper())
continue
left_shift = findShift(line, mode)
if left_shift == 0:
fa_file_output.write(line)
continue
new_header = "|".join([replaceHeader(elt, left_shift) for elt in line.split("|")])
fa_file_output.write(new_header)
fa_file.close()
fa_file_output.close()
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