def main(args):
fwig = gs.loadWig( args.forwardWig, smooth=False )
rwig = gs.loadWig( args.reverseWig, smooth=False )
mappedCount = getMappedCount(fwig, rwig)
poses = loadPos( args.positionFile, args.chromCol, args.startCol, args.endCol, args.strandCol, args.offset, args.format )
values = []
#print "\n"
#print fwig.keys()
#print rwig.keys()
for chrom in poses:
#print "\n"
#print chrom
if chrom in fwig:
chromFwig = gs.expandWig( fwig[ chrom ], 0, 1, False )
if chrom in rwig:
chromRwig = gs.expandWig( rwig[ chrom ], 0, 1, False)
chromPos = poses[ chrom ]
for p,strand in chromPos:
keep = True
tempFValues = np.zeros( 2 * args.width + 1 )
tempRValues = np.zeros( 2 * args.width + 1 )
if chrom in fwig:
#print chromFwig.shape
start = int(p - args.width - fwig[ chrom ][0,0])
end = int(p + args.width - fwig[ chrom ][0,0])
#print 'Forward'
#print start, " " , end
#print abs(min(0,start)), ' ', min( tempFValues.shape[0], tempFValues.shape[0] + chromFwig.shape[0] - end -1 )
#print max(0, start) , ' ', min( chromFwig.shape[0], end + 1 )
if end >= 0 and start < chromFwig.shape[0]:
tempFValues[abs(min(0,start)):min( tempFValues.shape[0], tempFValues.shape[0] + chromFwig.shape[0] - end -1) ] = chromFwig[ max(0, start) : min( chromFwig.shape[0], end + 1 ) ]
if chrom in rwig:
#print chromRwig.shape
start = int(p - args.width - rwig[ chrom ][0,0])
end = int(p + args.width - rwig[ chrom ][0,0])
#print 'Reverse'
#print start, " ", end
#print abs(min(0,start)), ' ', min( tempRValues.shape[0], tempRValues.shape[0] + chromRwig.shape[0] - end -1)
#print max(0, start) , ' ', min( chromRwig.shape[0], end + 1 )
if end >= 0 and start < chromRwig.shape[0]:
tempRValues[abs(min(0,start)):min( tempRValues.shape[0], tempRValues.shape[0] + chromRwig.shape[0] - end -1 ) ] = chromRwig[ max(0, start) : min( chromRwig.shape[0], end + 1 ) ]
thresh = mappedCount * args.thresh / 10**6
if tempRValues.sum() < thresh or tempFValues.sum() < thresh:
keep = False
if keep:
if strand == '-':
temp = tempFValues[::-1]
tempFValues = tempRValues[::-1]
tempRValues = temp
values.append(10**6*np.array(np.ma.concatenate([tempFValues, tempRValues])) / mappedCount)
values.sort(key=lambda k:(sum(k),))
writeAll( values, args.out + ".txt" )
values = np.array(values)
plot( values[:,0:2*args.width+1], values[:,2*args.width+1:], args.width, args.out )
def pair( fpeaks, rpeaks, fwig, rwig, ulimit, dlimit, prefix):
'''
Assuming that the peaks on one strand is mutually exclusive.
They do not overlap with each other.
In this case, the ordering of the starts of the peaks and the
ends of the peaks are the same. And that when the starts are
sorted, the ends are also sorted.
'''
offset = 5
expandCol = 1
out1 = open(prefix + "_singletons.bed",'w')
out2 = open(prefix + "_pairs.gff", "w")
out3 = open(prefix + "_pairs.narrowPeak", "w")
for chrom in fpeaks:
if chrom not in rpeaks:
continue
print chrom
fp = fpeaks[chrom]
rp = rpeaks[chrom]
pairF = [] #Store the pairing information, if unpaired, it will be negative.
pairR = []
fw = fwig[chrom]
expandedFw = gs.expandWig( fw, offset, expandCol, False )
rw = rwig[chrom]
expandedRw = gs.expandWig( rw, offset, expandCol, False )
rstarts = []
rends = []
fprefer = []
rprefer = []
unpairedF = []
for f in fp:
fprefer.append( SortedCollection( key=itemgetter(1) ) )
pairF.append( ( -1, 0, 0) ) #( index of the mate, score, distance )
for r in rp:
rprefer.append( SortedCollection( key=itemgetter(1) ) )
pairR.append( (-1, 0, 0) )
rstarts.append( r[1] )
rends.append( r[2] )
for i in range( len( fp ) ):
currfp = fp[ i ]
start = currfp[1]
end = currfp[2]
es = start - ulimit
ee = end + dlimit
currFw = expandedFw[ max( 0, start - fw[0,0] ) + offset : max( 0, end - fw[0,0] ) + offset + 1]
start = max( start, fw[0,0] )
end = max( end, fw[0,0] )
flength = end - start
si = bisect.bisect_left( rends, es )
ei = bisect.bisect_right( rstarts, ee )
ftagCounts,_,_ = gs.getTagCount( fwig, chrom, start, end )
#print ei - si
maxScore = 0
bestDist = 0
bestIdx = 0
bestRpos = 0
for idx in range( si, ei ):
currrp = rp[ idx ]
rstart = max(rw[0,0], currrp[1])
rend = min(rw[-1,0], currrp[2]+flength)
currRw = expandedRw[ max( 0, start - rw[0, 0] ) + offset : max( 0, rend - rw[0,0] ) + offset + 1 ]
rtagCoungs,_,_ = gs.getTagCount( rwig, chrom, currrp[1], currrp[2] )
tempScore, tempDist, tempRpos = getScore( currFw, currRw, start, rstart )
fprefer[ i ].insert( (idx, tempScore, tempDist, tempRpos) )
rprefer[ idx ].insert( (i, tempScore, tempDist, tempRpos) )
if tempScore > maxScore:
maxScore = tempScore
bestDist = tempDist
bestIdx = idx
bestRpos = tempRpos
if maxScore > pairR[ bestIdx ][1]:
pairF[i] = ( bestIdx, maxScore, bestDist , bestRpos)
if pairR[ bestIdx ][0] > 0:
unpairedF.append( pairR[ bestIdx ][0] )
pairR[bestIdx] = ( i, maxScore, bestDist, bestRpos )
else:
unpairedF.append( i )
try:
fprefer[ i ].remove( ( bestIdx, maxScore, bestDist, bestRpos ) )
except ValueError:
#print "Value error: ", bestIdx, ' ',maxScore, ' ',bestDist,' ', si,' ', ei
pass
singletons = []
pairs = []
pairs_narrow = []
while len(unpairedF) > 0:
for u in unpairedF:
if len( fprefer[u] ) > 0:
ridx = fprefer[u][-1][0]
if pairR[ ridx ][1] < fprefer[u][-1][1]:
if pairR[ idx ][0] > 0:
pairF[ pairR[ idx ][0] ] = (-1, 0, 0)
unpairedF.append( pairR[ idx ][0] )
pairR[ ridx ] = ( u, fprefer[u][-1][1], fprefer[u][-1][2], fprefer[u][-1][3] )
pairF[ u ] = ( ridx, fprefer[u][-1][1], fprefer[u][-1][2], fprefer[u][-1][3] )
fprefer[u].remove( (ridx, fprefer[u][-1][1], fprefer[u][-1][2], fprefer[u][-1][3] ) )
else:
unpairedF.remove( u )
for i,f in enumerate(pairF):
fp[i][1] -= 1
currFp = fp[i]
if f[0] == -1:
singletons.append( fp[i] )
else:
rp[f[0]][1] -= 1
currRp = rp[f[0]]
#pairs.append( fp[i] )
#pairs.append( rp[f[0]] )
pairStart = (2*f[3] - f[2])/2
pairEnd = pairStart + 1
pairs.append( [fp[i][0],'.','.',pairStart-10, pairEnd+10,f[1],'.','.','cw_distance='+str(f[2]) ] )
half_len = int(f[2]/2)
narrowStart= max(currFp[1] + half_len, currRp[1] - half_len) - half_len
narrowEnd = min(currFp[2] + half_len, currRp[2] - half_len) + half_len
pairs_narrow.append([currFp[0], narrowStart, narrowEnd, currFp[3]+'_'+currRp[3], (currFp[4]+currRp[4])/2, '.', (currFp[6]+currRp[6])/2, (currFp[7]+currRp[7])/2, (currFp[8]+currRp[8])/2, f[3] - half_len - narrowStart, f[2]])
for i,f in enumerate(pairR):
rp[i][1] -= 1
if f[0] == -1:
singletons.append( rp[i] )
singletons.sort(key=lambda k:( k[0], k[1], k[2] ))
pairs.sort(key = lambda k:( k[0], k[1], k[2]))
print "singletons: ", len(singletons)
print "pairs: ", len(pairs)
for s in singletons:
out1.write('\t'.join([str(i) for i in s]))
out1.write('\n')
for p in pairs:
out2.write('\t'.join([str(i) for i in p]))
out2.write('\n')
for p in pairs_narrow:
out3.write('\t'.join([str(i) for i in p]))
out3.write('\n')
out1.close()
out2.close()
out3.close()
