def Main():
global args,out
CellLine=["H1"]
HM=("input","H3K27ac","H3K27me3","H3K36me3","H3K4me1","H3K4me3","H3K9me3")
marks=[]
dbi={}
args=ParseArg()
if args.output=="stdout":
out=sys.stdout
else:
try:
out=open(args.output,"w")
except IOError:
print >>sys.stderr,"can't open file ",args.output,"to write. Using stdout instead"
out=sys.stdout
for cell in CellLine:
for hm in HM:
mark=cell+"_"+hm
marks.append(mark)
dbi[mark]=DBI.init("/data/zhuxp/bam2x/data/bamlist/"+mark+".bamlist","bamlist")
for i,x in enumerate(TableIO.parse(args.input,args.input_format)):
print >>out,"QR\t",x
if i%100==0: print >>sys.stderr,"query %d entries\r"%i,
for mark in marks:
print >>out,mark,"\t"
for j in DBI.query(x,dbi[mark]):
print >>out,"HT\t",j
def Main():
global args,out
args=ParseArg()
if args.output=="stdout":
out=sys.stdout
else:
try:
out=open(args.output,"w")
except IOError:
print >>sys.stderr,"can't open file ",args.output,"to write. Using stdout instead"
out=sys.stdout
dbi=DBI.init(args.db,args.dbformat)
for x in TableIO.parse(args.input,args.input_format):
print "QR\t",x
for j in DBI.query(x,dbi):
print "HT\t",j
x.chr=x.chr.replace("chr","")
for j in DBI.query(x,dbi):
print "HT\t",j
