def get_nlinks_dict(c1,bams,name2index,args,ll={}):
count={}
# index2=name2index[c2]
for sam in bams:
print("{}:{}-{}".format(c1,0,int(ll[c1])-1))
for aln in sam.fetch(reference=c1):
if (not aln.is_duplicate) and (aln.mapq >= args.mapq) and (BamTags.mate_mapq(aln) >= args.mapq):
count[aln.rnext]=count.get(aln.rnext,0)+1
return count
def chicago_pairs(sca,mapper,bamlist,minq=20,mask={}):
for seg in mapper.scaffold_contigs[sca]:
ref="_".join(seg.split("_")[:-1])
for b in bamlist:
for aln in b.fetch(until_eof=True,reference=ref):
if not aln.is_read1: continue
if aln.is_duplicate: continue
if aln.mapq < minq : continue
if BamTags.mate_mapq(aln) < minq : continue
# print("#x",ref,mask.get(ref,[]))
if mask_test(ref,aln.pos,mask) or mask_test(b.getrname(aln.rnext),aln.pnext,mask) : continue
contig = b.getrname(aln.tid) # snam[aln.tid]
ncontig= b.getrname(aln.rnext) if aln.rnext>=0 else -1
scaffold ,z1a,z2a,z3a,c1 = mapper.mapCoord( contig, aln.pos, aln.pos+1 )
nscaffold,z2p,x2p,z3p,c2 = mapper.mapCoord(ncontig, aln.pnext,aln.pnext+1 )
if debug: print(("#x",contig,ncontig,aln.pos,aln.pnext,scaffold,nscaffold,sca,z1a,z2p,ref,mapper.ocontig_contigs.get(ref,[])))
if scaffold==nscaffold and sca==scaffold:
#yield( sc,seg,contig,ncontig,scaffold,z1a,z2a,z3a,nscaffold,z2p,x2p,z3p )
yield( sca,z1a,z2p,c1,c2,seg,contig,ncontig,scaffold,z1a,z2a,z3a,nscaffold,z2p,x2p,z3p,aln.query_name )
#
if c1[-1]=="3":
k1 = contig_seq[c1[:-2]][-args.kmer:]
else:
k1 = rc(contig_seq[c1[:-2]][:args.kmer])
if c2[-1]=="5":
k2 = contig_seq[c2[:-2]][:args.kmer]
else:
k2 = rc(contig_seq[c2[:-2]][-args.kmer:])
print("\t".join(map(str,["gS:",sc,int(xx),c1,c2,c1[-1],c2[-1],k1,k2,k1 in seq, k2 in seq,"{}:{}".format(seq,qal),st,aln.is_reverse])))
#if overlaps_gap(aln2scaffoldx(aln)):
#pass
# this read overlapps a gap?
#OPEN:Scaffold278839 isotig431029.5 TTTTTCTCATCAGTCTCCTCATCACAAGTTTTCTATAAGTCCCCA isotig1560433.5 TTAAATCATAGCAGTACTCATGAAGAGGGTAGTAAAGCACTGGAA 57 14 : AG
if (not args.direct) and (not args.twopass) and (BamTags.mate_mapq(aln)>=10.0 and nscaffold in my_scaffolds) : # we might want this read because it's sister maps to one of our scaffolds
sc,xx,yy,st,cdz = mapper.mapCoord( ncontig,aln.pnext,aln.pnext+1 )
mate_scaffold_strand = st if not aln.mate_is_reverse else -1*st
if mate_scaffold_strand == -1:
xx -= insert_size
yy -= insert_size
else:
xx += insert_size
yy += insert_size
gaps = mapper.hits_gaps(sc,xx-400,yy+400)
if args.debug: print("#",gaps)
if gaps:
seq = aln.seq
qal = aln.qual
if mate_scaffold_strand==1:
seq = rc(seq)
buff = 0 #args.trim
for contig in contigs:
if args.debug: print("#{}".format(contig))
if (not contig in llen) or llen[contig] < args.minlen: continue
spans = []
edges = []
nb = []
lll = llen[contig]
# print "#",contig
for sam in bams:
for aln in sam.fetch(region=contig):
if (aln.tid == aln.rnext) and (aln.pos < aln.pnext) and (
(not args.ignoreDuplicates) or
(not aln.is_duplicate)) and (aln.mapq >= args.mapq) and (
BamTags.mate_mapq(aln) >= args.mapq):
# spans.append( tuple( [aln.pos, aln.pos+aln.tlen,aln.mapq,oname[sam]] ) )
# if aln.tlen > 2*buff and aln.tlen < range_cutoff:
if aln.tlen > 2 * buff: # and aln.tlen < range_cutoff:
ll = ces.model.lnF(aln.tlen)
# ll=get_score( aln.tlen )
edges.append(tuple([aln.pos + buff, ll]))
edges.append(
tuple([min(lll, aln.pos + aln.tlen - buff), -ll]))
nb.append(tuple([aln.pos + buff, 1]))
nb.append(
tuple([min(lll, aln.pos + aln.tlen - buff), -1]))
edges.sort()
nb.sort()
alniter = alngenerator()
else:
alniter = sam.fetch(until_eof=True)
for aln in alniter:
# print aln.pos, dir(aln)
nr+=1
if nr%200000 == 0:
sys.stderr.write("%d\n"%nr)
i,j = aln.tid, aln.rnext
if args.debug: print([i,j,int(aln.mapq),aln.tlen,aln.is_duplicate])
if int(aln.mapq) < args.min_qual: continue
if BamTags.mate_mapq(aln) < args.min_qual: continue
if aln.is_duplicate : continue
if args.junctions and BamTags.junction(aln) != "T": continue
if i==j:
if (slen[i]<args.minlength) : continue
if aln.tlen < 0: continue
hist[aln.tlen] = hist.get(aln.tlen,0)+1
n+=1
else:
if (slen[i]<args.minlength) or (slen[j]<args.minlength) : continue
if not aln.is_read1: continue
x = min( aln.pos , slen[i] - aln.pos ) + min( aln.pnext,slen[j]-aln.pnext)
hist2[x] = hist2.get(x,0)+1
n2+=1
def bam2chicagolinks(bamlist,
my_contigs,
smap,
mask_ranges,
mapq,
minl,
internal=False,
tidlist=False):
# print("bam2chicagolinks")
# if not smap: smap=SegMapper("/dev/null")
# print(my_contigs)
# print(smap)
# print(smap.segment_info)
for seg in my_contigs.keys():
if not smap:
ti = bamlist[0].references.index(seg)
l1 = bamlist[0].lengths[ti]
links = {}
tids = {}
if smap:
scaffold, x, y = smap.get_segment_info(seg)
region = "{}:{}-{}".format(scaffold, x, y)
else:
region = seg
x = -1
y = -1
print("#", seg, region)
for bam in bamlist:
#print(region)
for a in bam.fetch(region=region):
if a.mapq < mapq: continue
if a.is_duplicate: continue
if BamTags.mate_mapq(a) < mapq: continue
c1, c2, xx, yy = a.tid, a.rnext, a.pos, a.pnext
if xx < x: continue #print("#wtf?")
c1 = bam.getrname(c1)
c2 = bam.getrname(c2)
if mask_test(c1, xx, mask_ranges): continue
if mask_test(c2, yy, mask_ranges): continue
#print a
i = 0
if smap:
c2, yyy = smap.map_coord(c2, yy)
else:
yyy = yy
if c2 == seg and not internal: continue
if not smap and not c1 == c2: continue
#print( seg,c2,1+xx-x,1+yy-z)
#if 1+xx-x<0: print ("#?",region,scaffold,1+xx-x,x,y,seg,c1,xx,x,yy,z)
links[c2] = links.get(c2, []) + [(1 + xx - x, yyy)]
tids[c2] = tids.get(c2, []) + [a.query_name]
for c2 in links.keys():
if False and not c2 in smap.seg2len:
print(
"that's weird: {} not in table of segment lengths?".format(
c2))
raise Exception
if smap and not c2 in smap.seg2len: continue
if smap:
if (smap.seg2len.get(seg) > minl
and smap.seg2len.get(c2) > minl):
if tidlist:
yield ((seg, c2, smap.seg2len.get(seg),
smap.seg2len.get(c2), len(links[c2]),
links[c2], tids[c2]))
else:
yield ((seg, c2, smap.seg2len.get(seg),
smap.seg2len.get(c2), len(links[c2]),
links[c2]))
else:
# print(seg,c2,l1,l1,len(links[c2]),links[c2])
if tidlist:
yield ((seg, c2, l1, l1, len(links[c2]), links[c2],
tids[c2]))
else:
yield ((seg, c2, l1, l1, len(links[c2]), links[c2]))
"{}:{}".format(seq, qal),
st,
aln.is_reverse,
],
)
)
)
# if overlaps_gap(aln2scaffoldx(aln)):
# pass
# this read overlapps a gap?
# OPEN:Scaffold278839 isotig431029.5 TTTTTCTCATCAGTCTCCTCATCACAAGTTTTCTATAAGTCCCCA isotig1560433.5 TTAAATCATAGCAGTACTCATGAAGAGGGTAGTAAAGCACTGGAA 57 14 : AG
if (
(not args.direct)
and (not args.twopass)
and (BamTags.mate_mapq(aln) >= 10.0 and nscaffold in my_scaffolds)
): # we might want this read because it's sister maps to one of our scaffolds
sc, xx, yy, st, cdz = mapper.mapCoord(ncontig, aln.pnext, aln.pnext + 1)
mate_scaffold_strand = st if not aln.mate_is_reverse else -1 * st
if mate_scaffold_strand == -1:
xx -= insert_size
yy -= insert_size
else:
xx += insert_size
yy += insert_size
gaps = mapper.hits_gaps(sc, xx - 400, yy + 400)
if args.debug:
print("#", gaps)
if gaps:
seq = aln.seq
qal = aln.qual
def get_nlinks_spanning(c1,xx,ll,bams,name2index,args,gap):
l1=ll[c1]
count=0
# index2=name2index[c2]
for sam in bams:
for aln in sam.fetch(region=c1):
if (aln.rnext==aln.tid) and (not aln.is_duplicate) and (aln.mapq >= args.mapq) and (BamTags.mate_mapq(aln) >= args.mapq) and (aln.pos<xx-old_div(gap,2)) and (aln.pnext>xx+old_div(gap,2)):
count+=1
return count
def get_nlinks(c1,c2,ll,bams,name2index,args):
l1=ll[c1]
l2=ll[c2]
if l2<l1:
x = c1
c1= c2
c2= x
count=0
index2=name2index[c2]
for sam in bams:
for aln in sam.fetch(region=c1):
if (aln.rnext==index2) and (not aln.is_duplicate) and (aln.mapq >= args.mapq) and (BamTags.mate_mapq(aln) >= args.mapq):
count+=1
return count
llen={}
for i in range(len(snam)):
llen[snam[i]]=slen[i]
buff=0 #args.trim
for contig in contigs:
if args.debug: print("#{}".format(contig))
if (not contig in llen) or llen[contig]<args.minlen: continue
spans=[]
edges=[]
nb=[]
lll = llen[contig]
# print "#",contig
for sam in bams:
for aln in sam.fetch(region=contig):
if (aln.tid==aln.rnext) and (aln.pos<aln.pnext) and ((not args.ignoreDuplicates) or (not aln.is_duplicate)) and (aln.mapq >= args.mapq) and (BamTags.mate_mapq(aln) >= args.mapq):
# spans.append( tuple( [aln.pos, aln.pos+aln.tlen,aln.mapq,oname[sam]] ) )
# if aln.tlen > 2*buff and aln.tlen < range_cutoff:
if aln.tlen > 2*buff: # and aln.tlen < range_cutoff:
ll=ces.model.lnF(aln.tlen)
# ll=get_score( aln.tlen )
edges.append( tuple([aln.pos + buff , ll]) )
edges.append( tuple([min(lll,aln.pos+aln.tlen-buff) ,-ll]) )
nb.append( tuple([aln.pos + buff , 1]) )
nb.append( tuple([min(lll,aln.pos+aln.tlen-buff) ,-1]) )
edges.sort()
nb.sort()
rs=0
n=0
def bam2chicagolinks(bamlist,my_contigs,smap,mask_ranges,mapq,minl,internal=False,tidlist=False):
# print("bam2chicagolinks")
# if not smap: smap=SegMapper("/dev/null")
# print(my_contigs)
# print(smap)
# print(smap.segment_info)
for seg in my_contigs.keys():
if not smap:
ti=bamlist[0].references.index(seg)
l1 = bamlist[0].lengths[ti]
links = {}
tids = {}
if smap:
scaffold,x,y = smap.get_segment_info(seg)
region = "{}:{}-{}".format(scaffold,x,y)
else:
region = seg
x=-1
y=-1
print("#",seg,region)
for bam in bamlist:
#print(region)
for a in bam.fetch(region=region):
if a.mapq<mapq: continue
if a.is_duplicate: continue
if BamTags.mate_mapq(a)<mapq: continue
c1,c2,xx,yy = a.tid,a.rnext,a.pos,a.pnext
if xx<x: continue #print("#wtf?")
c1 = bam.getrname(c1)
c2 = bam.getrname(c2)
if mask_test(c1,xx,mask_ranges): continue
if mask_test(c2,yy,mask_ranges): continue
#print a
i=0
if smap:
c2,yyy = smap.map_coord(c2,yy)
else:
yyy=yy
if c2==seg and not internal : continue
if not smap and not c1==c2: continue
#print( seg,c2,1+xx-x,1+yy-z)
#if 1+xx-x<0: print ("#?",region,scaffold,1+xx-x,x,y,seg,c1,xx,x,yy,z)
links[c2] = links.get(c2,[]) + [( 1+xx-x,yyy )]
tids[c2] = tids.get(c2,[]) + [ a.query_name ]
for c2 in links.keys():
if False and not c2 in smap.seg2len:
print ("that's weird: {} not in table of segment lengths?".format(c2))
raise Exception
if smap and not c2 in smap.seg2len: continue
if smap:
if (smap.seg2len.get(seg)>minl and smap.seg2len.get(c2)>minl):
if tidlist:
yield( (seg,c2,smap.seg2len.get(seg),smap.seg2len.get(c2),len(links[c2]),links[c2], tids[c2]) )
else:
yield( (seg,c2,smap.seg2len.get(seg),smap.seg2len.get(c2),len(links[c2]),links[c2]) )
else:
# print(seg,c2,l1,l1,len(links[c2]),links[c2])
if tidlist:
yield( (seg,c2,l1,l1,len(links[c2]),links[c2],tids[c2]) )
else:
yield( (seg,c2,l1,l1,len(links[c2]),links[c2] ) )