import random,os
import glob, os, sys

fn=sys.argv[1] # fusion gene information file

inf=open(fn,'r')
outf=open(fn.split('.')[0]+'.FusionAI.input','w')

while 1:
	line=inf.readline()
	if not line: break

	gs=line[:-1].split('\t')
	g1=gs[0]
	str1=gs[3]
	chr1=gs[1]
	bp1=int(gs[2])

	g2=gs[4]
	chr2=gs[5]
	bp2=int(gs[6])
	str2=gs[7]

	str1_=''
	str2_=''
	if str1!='' and str2!='':
		if str1=='-':
			str1_='m'
		else:
			str1_='+'
		if str2=='-':
			str2_='m'
		else:
			str2_='+'

		a=g1+'_'+str(bp1)+'_'+g2+'_'+str(bp2)
		os.system('./nibFrag -upper ./nib_files_hg19/'+chr1+'.nib '+str(bp1-5000)+' ' +str(bp1+5000) +' '+str1_+' seq1_.fa')
		os.system('sleep 1')
		os.system('./nibFrag -upper ./nib_files_hg19/'+chr2+'.nib '+str(bp2-5000)+' ' +str(bp2+5000) +' '+str2_+' seq2_.fa')
		os.system('sleep 1')


		seq1=''
		seq2=''
		inf_in1=open('seq1_.fa','r')
		inf_in2=open('seq2_.fa','r')
		while 1:
			line2=inf_in1.readline()
			if not line2: break
			if line2[0]!='>':
				seq1+=line2[:-1]
		while 1:
			line2=inf_in2.readline()
			if not line2: break
			if line2[0]!='>':
				seq2+=line2[:-1]

		T=g1+'\t'+chr1+'\t'+str(bp1)+'\t'+str1+'\t'+g2+'\t'+chr2+'\t'+str(bp2)+'\t'+str2+'\t'+seq1+'\t'+seq2+'\n'
		outf.write(T)
		outf.flush()