p=argparse.ArgumentParser(description="get intensity of epi-modification on single nucleosome",epilog="library dependency: xplib")

p.add_argument("-N","--Nucleosome",dest="nucleosome",type=str,help="xls file containing nucleosome location information from Danpos output")

p.add_argument("-b","--bams",nargs='+',dest="bams",type=str,help="bed/bam files for epigenetic data")

p.add_argument('-f','--fmt',type=str,default='bam',help='format: bed/bam,default:bam')

p.add_argument("-l","--length",dest="len",type=int,default=200,help="average length of ChIP-seq fragment,default:200")

p.add_argument("-n","--name",nargs='+',dest='name',type=str,help='name of each bam/bed sample (to be wrote on the header)')

p.add_argument('-r','--rangeS',type=int,default=100,help='search range to find the maximum Epi-intensity in each nucleosome location (default: 100bp)')

p.add_argument("-w","--weightP",nargs='+',dest='weightP',type=int,default=[75,125],help='parameters to calculate the weight for each read,[half_len of core nucleosome region and half_len of whole regions],default: [75,125]')

p.add_argument("-o","--output",dest="output",type=str,help="output file name (can be .txt)")

p.add_argument("-v",'--verbose',action='store_true',help='set to output shifted nucleosome centers for each histone mark, one bed file per mark')

if len(sys.argv)==1:

print >>sys.stderr,p.print_help()

exit(0)

# read.id in strand for bed with for columns

if fmt=='bed':

strand=read.id

elif fmt=='bam':

strand=read.strand

if strand=="+":

center=read.start+half_len

elif strand=="-":

center=read.stop-half_len

else:

print >>sys.stderr,read.id,"No strand"

# get the count of each epi-mark in each nucleosome by searching from [nuc_center-rangeS, nuc_center+rangeS]

# stepsize: 5bp

max_count=0

offset=-rangeS

for off in range(-rangeS,rangeS,5):

count=0

for j_center in read_centers:

weight = max(min(1,(ma-abs(j_center-(center+off)))*1.0/(ma-mi)),0)

count+=weight

if (count>max_count) or ((count>=max_count) and (abs(off)<abs(offset))): # choose the offset with largest count and smallest offset

max_count=count

offset=off

args=ParseArg()

#store bed files with indexing and count information:

bam={}

print >>sys.stderr,"Starting index bam/bed files:"

for i in range(len(args.bams)):

temp_name=args.name[i]

print >>sys.stderr," #Indexing for bam/bed file of",temp_name,"\r",

bam[temp_name]=DBI.init(args.bams[i],args.fmt)

print >>sys.stderr

print >>sys.stderr,"Reading nucleosome peak xls file from Danpos."

nucleosomes=TableIO.parse(args.nucleosome,'metabed',header=True)

print >>sys.stderr,"Initial output files..."

out=open(args.output,"w")

# -- for verbose ---

if args.verbose:

out_mark=[]

for n in args.name:

out_mark.append(open(n+'_shift_nucleosomes.bed','w'))

# ------------------

line_head=open(args.nucleosome,'r').readline().strip()

line_head=line_head+"\t"+"\t".join(str(f) for f in args.name)+'\t'+"\t".join(str(f)+'_off' for f in args.name)

print >>out,line_head

print >>sys.stderr,"Start Counting..."

num=0

t0 = time()

for i in nucleosomes:

chrom=i.chr

if i.smt_pval>0.01 or i.fuzziness_pval>0.01: continue # only choose nucleosomes with high value and low fuzziness

if "random" in chrom or chrom == 'chrM':

continue

num=num+1

center=int(i.start+i.end)/2

count=np.zeros(len(args.bams),dtype="float")

offset=np.zeros(len(args.bams),dtype='int')

line=str(i)

for k,name in enumerate(args.name):

if args.fmt=='bam':

query=bam[name].query(Bed([chrom,center-ma-(half_len-75)-rangeS,center+ma+(half_len-75)+rangeS]),method='fetch')

else:

query=bam[name].query(Bed([chrom,center-ma-(half_len-75)-rangeS,center+ma+(half_len-75)+rangeS]))

read_centers=[]

for j in query:

read_centers.append(find_center(j,args.fmt))

[o,c]=getCount(read_centers,center)

count[k]=c

offset[k]=o

# -- for verbose ---

if args.verbose:

print >>out_mark[k],chrom+'\t%d\t%d'%(i.start+o,i.end+o)

# ------------------

line = line + "\t" + "\t".join(str(f) for f in count) + '\t' + "\t".join(str(f) for f in offset)

if num%20000==0:

t1 = time()

print >>sys.stderr,"processing %dth nucleosome..., time: %.2fs."%(num,t1-t0),'\r',

t0 = time()

print >>out,line

print

out.close()

# -- for verbose ---

if args.verbose:

for k in out_mark:

k.close()