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#!/usr/bin/python3
import sys
import os
import subprocess
from parse_read import *
from parse_alignment import *
filename,filename2 = sys.argv[1:3]
alignmentname = sys.argv[3]
readarg = sys.argv[4]
k = int(sys.argv[5])
stream = subprocess.Popen(["LA4Awesome", filename, filename2 , alignmentname ,readarg],
stdout=subprocess.PIPE, bufsize=1)
alignments = parse_alignment2(stream.stdout) # generator
d = {}
for alignment in alignments:
if alignment[2] not in d:
d[alignment[2]] = []
d[alignment[2]].append([alignment[0],alignment[3],alignment[4], alignment[6], alignment[7], alignment[1]])
#print d
mapping = {}
for key,value in list(d.items()):
value.sort(key = lambda x:x[2]-x[1], reverse=True)
alns = value[:k]
max_val=alns[0][2]-alns[0][1]
for aln in alns:
if aln[2]-aln[1] > max_val/2.:
if str(key) not in mapping:
mapping[str(key)] = [(aln[1], aln[2],aln[-1], 1-int(aln[0] == 'n'))]
# mapping[str(key)+'\''] = [(aln[2], aln[1],aln[-1], int(aln[0] == 'n'))]
else:
mapping[str(key)].append((aln[1], aln[2],aln[-1], 1-int(aln[0] == 'n')))
# mapping[str(key)+'\''].append((aln[2], aln[1],aln[-1], int(aln[0] == 'n')))
#print mapping
import ujson
ujson.dump(mapping,open(filename2+'.mapping.'+str(k)+'.json','w'))
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