Eric Coissac
ae703c70d6
Former-commit-id: 55a83611220f824a0efdb1267816f98df984152e Former-commit-id: e01bf6440c2981904f31807766e9e48aea8b18c1
136 lines
3.8 KiB
Python
Executable File
136 lines
3.8 KiB
Python
Executable File
#!/usr/bin/env python
|
|
|
|
import sys
|
|
|
|
data = open(sys.argv[1])
|
|
repeats = open(sys.argv[2])
|
|
|
|
chloro = {'LSC' : [], 'SSC' : [] }
|
|
chlorosize =0
|
|
|
|
for line in data:
|
|
parts = line.strip().split()
|
|
if len(parts) >= 4:
|
|
single = parts[0]
|
|
begin = int(parts[1])
|
|
end = int(parts[2])
|
|
direction = int(parts[3])
|
|
|
|
|
|
if direction==0:
|
|
direction=-1
|
|
|
|
if end > chlorosize:
|
|
extsize = end - chlorosize
|
|
chloro['LSC'].extend([0] * extsize)
|
|
chloro['SSC'].extend([0] * extsize)
|
|
chlorosize=len(chloro['LSC'])
|
|
|
|
begin-=1
|
|
|
|
chr = chloro[single]
|
|
|
|
for p in range(begin,end):
|
|
chr[p]+=direction
|
|
|
|
maxSSC = float(max(abs(n) for n in chloro['SSC']))
|
|
maxLSC = float(max(abs(n) for n in chloro['LSC']))
|
|
|
|
chloro['SSC']=[n / maxSSC for n in chloro['SSC']]
|
|
chloro['LSC']=[n / maxLSC for n in chloro['LSC']]
|
|
|
|
|
|
scoreMax=0
|
|
imax = len(chloro['LSC'])
|
|
|
|
for line in repeats:
|
|
parts = line.strip().split()
|
|
|
|
pos1 = int(parts[1]) -1
|
|
len1 = int(parts[3])
|
|
|
|
pos2 = int(parts[2]) -1
|
|
len2 = int(parts[4])
|
|
|
|
c_begin = min(pos1 + len1,imax)
|
|
c_end = min(pos2,imax)
|
|
o_max = min(pos1 ,imax)
|
|
o_min = min(pos2 + len2, imax)
|
|
|
|
c_lsc = sum(abs(chloro['LSC'][n]) for n in range(c_begin,c_end))
|
|
c_ssc = sum(abs(chloro['SSC'][n]) for n in range(c_begin,c_end))
|
|
|
|
o_lsc = sum(abs(chloro['LSC'][n]) for n in range(0,o_max))
|
|
o_ssc = sum(abs(chloro['SSC'][n]) for n in range(0,o_max))
|
|
|
|
o_lsc += sum(abs(chloro['LSC'][n]) for n in range(o_min,len(chloro['LSC'])))
|
|
o_ssc += sum(abs(chloro['SSC'][n]) for n in range(o_min,len(chloro['SSC'])))
|
|
|
|
c = float(c_lsc + c_ssc)
|
|
o = float(o_lsc + o_ssc)
|
|
|
|
if c > 0:
|
|
c_lsc /= c
|
|
c_ssc /= c
|
|
|
|
if o > 0:
|
|
o_lsc /= o
|
|
o_ssc /= o
|
|
|
|
score = ((c_lsc - c_ssc) ** 2 + (o_lsc - o_ssc) ** 2) / 2.0
|
|
|
|
# print >>sys.stderr,"c.lsc = %f c.ssc = %f o.lsc = %f o.ssc = %f score = %6.4f (len=%d)" % (c_lsc,c_ssc,o_lsc,o_ssc,score,len1)
|
|
|
|
if (score > scoreMax):
|
|
scoreMax = score
|
|
pos1Max = pos1
|
|
pos2Max = pos2
|
|
len1Max = len1
|
|
len2Max = len2
|
|
|
|
c_begin = min(pos1Max + len1Max,imax)
|
|
c_end = min(pos2Max,imax)
|
|
o_max = min(pos1Max,imax)
|
|
o_min = min(pos2Max + len2Max,imax)
|
|
|
|
c_lsc = sum(chloro['LSC'][n] for n in range(c_begin,c_end))
|
|
c_ssc = sum(chloro['SSC'][n] for n in range(c_begin,c_end))
|
|
|
|
o_lsc = sum(chloro['LSC'][n] for n in range(0,o_max))
|
|
o_ssc = sum(chloro['SSC'][n] for n in range(0,o_max))
|
|
|
|
o_lsc += sum(chloro['LSC'][n] for n in range(o_min,len(chloro['LSC'])))
|
|
o_ssc += sum(chloro['SSC'][n] for n in range(o_min,len(chloro['SSC'])))
|
|
|
|
if abs(c_lsc) > abs(c_ssc):
|
|
center = "LSC"
|
|
dcenter= "+" if c_lsc > 0 else "-"
|
|
else:
|
|
center = "SSC"
|
|
dcenter= "+" if c_ssc > 0 else "-"
|
|
|
|
if abs(o_lsc) > abs(o_ssc):
|
|
out = "LSC"
|
|
dout = "+" if o_lsc > 0 else "-"
|
|
else:
|
|
out = "SSC"
|
|
dout = "+" if o_ssc > 0 else "-"
|
|
|
|
|
|
|
|
sys.stdout.write("%s %s %s %s %d %d %d %d %6.5f\n" % (center,
|
|
dcenter,
|
|
out,
|
|
dout,
|
|
pos1Max + 1,
|
|
len1Max,
|
|
pos2Max + 1,
|
|
len2Max,
|
|
scoreMax))
|
|
|
|
|
|
|
|
#for p in range(chlorosize):
|
|
# sys.stdout.write("%d %d %d\n" % (p,chloro['SSC'][p],chloro['LSC'][p]))
|
|
|