PhyloSkims/annotate
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Patch bug in the inverted repeats annotation

Browse Source 
Realize the annotation on the normalized chromosome


Former-commit-id: 73e4e016d7bfe23fc92e4071efb0a4629eb8e21f
Former-commit-id: d44249c0d078d475ca80386bb428fb660289b0dd
This commit is contained in:
Eric Coissac
2015-11-09 17:03:22 +01:00
parent 58e99a81eb
commit 195739b5f8
4 changed files with 53 additions and 20 deletions
Download Patch File Download Diff File Expand all files Collapse all files

49
detectors/normalize/lib/selectIR.py
View File

@ -8,6 +8,12 @@ repeats = open(sys.argv[2])
chloro = {'LSC' : [], 'SSC' : [] }
chlorosize =0
# We scan the blast matches:
# We build a vector with one position per base pair counting the matches
# The match file has the following format:
# LSC/SSC begin end same_strand=1/diff_strand=0
for line in data:
parts = line.strip().split()
if len(parts) >= 4:
@ -16,7 +22,8 @@ for line in data:
end = int(parts[2])
direction = int(parts[3])
# Change the code of the direction:
# reverse complement = -1
if direction==0:
direction=-1
@ -39,36 +46,53 @@ 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
len1Max=0
len2Max=0
imax = len(chloro['LSC'])
for line in repeats:
parts = line.strip().split()
# First repeat position and length
# (position start at 0)
pos1 = int(parts[1]) -1
len1 = int(parts[3])
# Second repeat position and length
# (position start at 0)
pos2 = int(parts[2]) -1
len2 = int(parts[4])
# Location of the central single copy
# - in between the two IR -
c_begin = min(pos1 + len1,imax)
c_end = min(pos2,imax)
# Location of the external single copy
# - in between the two IR -
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))
# count of coherent matches for LSC and SSC on the central single copy
c_lsc = abs(sum(chloro['LSC'][n] for n in range(c_begin,c_end)))
c_ssc = abs(sum(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))
# count of coherent matches for LSC and SSC on the external single copy
# this score is in two parts before the first copy and after the second
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(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'])))
o_lsc += sum(chloro['LSC'][n] for n in range(o_min,imax))
o_ssc += sum(chloro['SSC'][n] for n in range(o_min,imax))
o_lsc = abs(o_lsc)
o_ssc = abs(o_ssc)
c = float(c_lsc + c_ssc)
o = float(o_lsc + o_ssc)
if c > 0:
c_lsc /= c
c_ssc /= c
@ -78,10 +102,9 @@ for line in repeats:
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):
if (score >= scoreMax) and ((len1 > len1Max) or (len2 > len2Max)):
scoreMax = score
pos1Max = pos1
pos2Max = pos2
@ -99,8 +122,8 @@ 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'])))
o_lsc += sum(chloro['LSC'][n] for n in range(o_min,imax))
o_ssc += sum(chloro['SSC'][n] for n in range(o_min,imax))
if abs(c_lsc) > abs(c_ssc):
center = "LSC"