def validate(signals,chrom):
juncfile = os.path.join(juncDir,'supposed.rawbin.splicemap.%s.new.bed'%(chrom,))
out = readBed.BEDWriter(os.path.join(outDir,chrom+'_recovered.bed'))
junctions = calJuncCoverage.getJunctions(juncfile)
global validated
for junc in junctions:
leftindex = junc['chromStart'] + junc['blockSizes'][0] - 1
rightindex = junc['chromStart'] + junc['blockStarts'][1]
key = '_'.join([junc['chrom'],str(leftindex),str(rightindex)])
if key in signals:
out.writerow(junc)
validated += 1
"python26 calJuncCoverage.py -s -j %s -r %s -a %d -c %d -o %s"
% (currJuncFile, spliceReadFile, 10, 15, spliceoutfile)
)
tophatoutfile = os.path.join(outputdir, "tophat_chr%s.txt" % (str(i),))
os.system("echo tophat")
os.system(
"python26 calJuncCoverage.py -s -j %s -r %s -a %d -c %d -o %s"
% (currJuncFile, tophatReadFile, 10, 15, tophatoutfile)
)
simulatedoutfile = os.path.join(outputdir, "simulated_chr%s.txt" % (str(i),))
os.system("echo original_reads")
os.system(
"python26 calJuncCoverage.py -s -j %s -r %s -a %d -c %d -o %s"
% (currJuncFile, simulatedReadFile, 0, 15, simulatedoutfile)
)
tempjunctions, tempsignals = calJuncCoverage.getJunctions(currJuncFile, True)
for sig in tempsignals:
sigRev = ""
for base in sig:
sigRev = BASE[base] + sigRev
if sig in signals:
signals[sig] += tempsignals[sig]
elif sigRev in signals:
signals[sigRev] += tempsignals[sig]
else:
signals[sig] = tempsignals[sig]
os.system("echo ")
print "\n----------------------Summary---------------------------"
for key in signals:
print key, " ", signals[key]
