python28

# -*- coding: utf-8 -*-

import os
import sys
import re

in1=sys.argv[1]
out1=sys.argv[2]

ouc=open(out1,'w')

with open(in1,'r') as i:
    li=i.readlines()
    for lin in li:
        linc=lin.strip().split("\t")
        pos1=str(linc[2])
        pos2=str(linc[6])
        matchcon=str(linc[5])
        posID=str(linc[0])
        con1=str(linc[5]).strip().split("M")
        result=con1[0]
        if result.isdigit():
            if "chr" in str(pos1) and "virus" in str(pos2) and "150M" not in str(matchcon):
                posinsert=int(linc[3])+int(result)
                ouc.write(str(linc[0])+"\t"+str(linc[2])+"\t"+str(posinsert)+"\n")
            elif "chr" in str(pos2) and "virus" in str(pos1) and "150M" not in str(matchcon):
                posinsert=int(linc[7])+int(result)
                ouc.write(str(linc[0])+"\t"+str(linc[6])+"\t"+str(posinsert)+"\n")
        con2=str(linc[5]).strip().split("S")
        result1=con2[0]
        if result1.isdigit():
            if "chr" in str(pos1) and "virus" in str(pos2) and "150M" not in str(matchcon):
                posinsert=int(linc[3])
                ouc.write(str(linc[0])+"\t"+str(linc[2])+"\t"+str(posinsert)+"\n")
            elif "chr" in str(pos2) and "virus" in str(pos1) and "150M" not in str(matchcon):
                posinsert=int(linc[7])
                ouc.write(str(linc[0])+"\t"+str(linc[6])+"\t"+str(posinsert)+"\n")

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import os
import sys
import re
from Bio import SeqIO
from Bio.Seq import Seq

in1=sys.argv[1]
ou1 = sys.argv[2]

seqdict={}
for seqi in SeqIO.parse('./homo.fa',"fasta"):
    seqid=seqi.id
    seqseq=seqi.seq
    seqdict[seqid]=seqseq

ouc=open(ou1,'w')
count=0
with open(in1,'r') as i:
    li=i.readlines()
    for lin in li:
        linc=lin.strip().split("\t")
        count=count+1
        poschr=linc[1]
        pospos=linc[2]
        basepos=seqdict[poschr][int(pospos)]
        ouc.write(str(linc[1])+"\t"+str(linc[2])+"\tINV0000000"+str(count)+"\t"+str(basepos)+"\t<INV>\t1\tPASS\tPRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.8.7;""\n")