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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]
stream = subprocess.Popen(["LA4Awesome", filename, filename2 , alignmentname ,readarg, '-F'],
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)
aln = value[0]
if aln[0] == 'n':
mapping[str(key)] = (aln[1], aln[2],aln[-1], 0)
mapping[str(key)+'\''] = (aln[2], aln[1],aln[-1], 1)
else:
mapping[str(key)] = (aln[2], aln[1], aln[-1], 1)
mapping[str(key)+'\''] = (aln[1], aln[2], aln[-1], 0)
#print mapping
import ujson
ujson.dump(mapping,open(filename+'.mapping.json','w'))
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