From 1c69f700a2dc4c82e9a5ebbc23cda8cd82779bc1 Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Wed, 23 Jun 2021 10:37:50 +1000
Subject: [PATCH] breakdown to modules and refactor
---
src/private/findpath.nim | 109 +++++++++++
src/private/graph.nim | 90 +++++++++
src/private/utils.nim | 108 +++++++++++
src/sscocaller.nim | 403 ++++++---------------------------------
4 files changed, 362 insertions(+), 348 deletions(-)
create mode 100755 src/private/findpath.nim
create mode 100755 src/private/graph.nim
create mode 100755 src/private/utils.nim
diff --git a/src/private/findpath.nim b/src/private/findpath.nim
new file mode 100755
index 0000000..cdbd8b9
--- /dev/null
+++ b/src/private/findpath.nim
@@ -0,0 +1,109 @@
+## implements the traceback function
+import utils
+from graph import SpermViNodes
+import streams
+import tables
+import math
+
+
+proc pathTrackBack*(currentSperm: var SpermViNodes,
+ ithSperm: int,
+ thetaRef: float,
+ thetaAlt: float,
+ cmPmb: float,
+ outFileVStateMtx: var FileStream,
+ viSegmentInfo: var FileStream,
+ posEnd: var int64,
+ inferProb: var float,
+ reverseProb: var float): int =
+ var currentEm,prevEm: array[stateRef..stateAlt, float]
+ var posStart:int64
+ var transitFlag = false
+ var cSNP = 1
+ var ithSNP: int
+ var transProb: float
+ var rightGap,leftGap: array[0..1, float]
+ for i in 1..high(currentSperm.viNodeseq):
+ var state = currentSperm.viNodeseq[^i].state
+ currentSperm.viNodeseq[^(i+1)].state = currentSperm.viNodeseq[^i].pathState[state]
+ prevEm = getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,
+ cRef=currentSperm.viNodeseq[^(i+1)].cRef,
+ cAlt=currentSperm.viNodeseq[^(i+1)].cAlt)
+ ithSNP = currentSperm.spermSnpIndexLookUp[high(currentSperm.viNodeseq)-i+1]
+ transProb = getTrans(currentSperm.viNodeseq[^(i+1)].pos,
+ currentSperm.viNodeseq[^(i)].pos,
+ cmPmb=cmPmb)
+ if currentSperm.viNodeseq[^(i+1)].state == stateRef:
+ outFileVStateMtx.writeLine($ithSNP & " " & $(ithSperm+1) & " 1")
+ if state == stateRef:
+ # not transitioning to a different state ie still in this segment of same state
+ inferProb+=prevEm[stateRef]
+ reverseProb+=prevEm[stateAlt]
+ cSNP += 1
+ transitFlag = false
+ #posStart = currentSperm[^(i+1)].pos
+ else: # there is transition to different state: ref(start) to alt(end) now output the segment info
+ posStart = currentSperm.viNodeseq[^(i)].pos
+ #leftGapSize = currentSperm[^(i)].pos - currentSperm[^(i+1)].pos
+ leftGap=[math.ln(transProb),math.ln(1-transProb)]
+ inferProb+=leftGap[0]
+ reverseProb+=leftGap[1]
+ viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 2")
+ transitFlag = true
+ cSNP = 1
+ rightGap = leftGap
+ inferProb = prevEm[stateRef]+rightGap[0]
+ reverseProb = prevEm[stateAlt]+rightGap[1]
+ posEnd = currentSperm.viNodeseq[^(i+1)].pos
+ else:
+ outFileVStateMtx.writeLine($ithSNP & " " & $(ithSperm+1) & " 2")
+ if state == stateAlt:
+ # not transitioning to a different state ie still in this segment of same state
+ inferProb += prevEm[stateAlt]
+ reverseProb += prevEm[stateRef]
+ cSNP += 1
+ transitFlag = false
+ else:
+ ## state transit
+ posStart = currentSperm.viNodeseq[^(i)].pos
+ leftGap=[math.ln(transProb),math.ln(1-transProb)]
+ inferProb += leftGap[0]
+ reverseProb += leftGap[1]
+ viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 1" )
+ transitFlag = true
+ cSNP = 1
+ rightGap = leftGap
+ inferProb = prevEm[stateAlt]+rightGap[0]
+ reverseProb = prevEm[stateRef]+rightGap[1]
+ posEnd = currentSperm.viNodeseq[^(i+1)].pos
+ ## traced to the start position of the chromosome for this cell
+ #leftGap = [0.0,0.0]
+ if not transitFlag:
+ ## the first SNP is included in the segment from traced from back
+ posStart = currentSperm.viNodeseq[0].pos
+ if currentSperm.viNodeseq[0].state == stateRef:
+ viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 1" )
+ else:
+ viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 2" )
+ else:
+ ## the first node has different state from the second, the first node has its own segment
+ posStart = currentSperm.viNodeseq[0].pos
+ posEnd = posStart
+ cSNP = 1
+ currentEm = getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,
+ cRef=currentSperm.viNodeseq[0].cRef,
+ cAlt=currentSperm.viNodeseq[0].cAlt)
+ transProb = getTrans(currentSperm.viNodeseq[0].pos,
+ currentSperm.viNodeseq[1].pos,
+ cmPmb=cmPmb)
+ if currentSperm.viNodeseq[0].state == stateRef:
+ inferProb = currentEm[stateRef]+math.ln(transProb)
+ reverseProb = currentEm[stateAlt]+math.ln(1-transProb)
+ viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 1" )
+ else:
+ inferProb = currentEm[stateAlt]+math.ln(transProb)
+ reverseProb = currentEm[stateRef]+math.ln(1-transProb)
+ viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 2" )
+
+
+ return 0
diff --git a/src/private/graph.nim b/src/private/graph.nim
new file mode 100755
index 0000000..4ebb0fb
--- /dev/null
+++ b/src/private/graph.nim
@@ -0,0 +1,90 @@
+import tables
+import utils
+import streams
+import hts
+import math
+
+type
+ # Nucleotide = enum
+ # A, C, T, G
+ SpermViNodes* = object
+ viNodeseq*: seq[ViNode]
+ ## look up from SNPIndex to current Sperm SNP index
+ snpIndexLookUp*: Table[int,int]
+ ## look up from current Sperm SNP index to SNPIndex
+ spermSnpIndexLookUp*: Table[int,int]
+ SeqSpermViNodes* = seq[SpermViNodes]
+
+
+proc addViNode*(barcodeTable: OrderedTableRef,
+ alleleCountTable: Table[string,allele_expr],
+ scSpermSeq: var SeqSpermViNodes,
+ outFileTotalCountMtx: var FileStream,
+ outFileAltCountMtx: var FileStream,
+ nnsize: var int,
+ mindp: int,
+ maxdp: int,
+ snpIndex: int,
+ thetaRef: float,
+ thetaAlt: float,
+ rec: Variant,
+ initProb: array,
+ cmPmb: float): int =
+ for bc, ac in alleleCountTable.pairs:
+ # ac.tostring(acs)
+ ## mindp, maxdp, they are values per cell
+ if (ac.cref+ac.calt) <= mindp or (ac.cref+ac.calt) >= maxdp: continue
+ var ithSperm = barcodeTable[bc]
+ ## write to mtx Ref count
+ outFileTotalCountMtx.writeLine($snpIndex & " " & $(ithSperm+1) & " " & $(ac.cRef+ac.cAlt))
+ outFileAltCountMtx.writeLine($snpIndex & " " & $(ithSperm+1) & " " & $ac.cAlt)
+ nnsize += 1
+ var emissionArray = getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,cRef=ac.cRef,cAlt=ac.cAlt)
+ if scSpermSeq[ithSperm].viNodeseq.len==0:
+ var currentViNode = ViNode()
+ currentViNode.pathScore[stateRef] = math.ln(initProb[stateRef])+emissionArray[stateRef]
+ currentViNode.pathScore[stateAlt] = math.ln(initProb[stateAlt])+emissionArray[stateAlt]
+ currentViNode.pathState[stateRef] = stateN
+ currentViNode.pathState[stateAlt] = stateN
+ currentViNode.state = stateN
+ currentViNode.pos = int(rec.POS)
+ currentViNode.cAlt = int(ac.cAlt)
+ currentViNode.cRef = int(ac.cRef)
+
+ scSpermSeq[ithSperm].viNodeseq.add(currentViNode)
+ scSpermSeq[ithSperm].snpIndexLookUp[snpIndex] = scSpermSeq[ithSperm].viNodeseq.len
+ scSpermSeq[ithSperm].spermSnpIndexLookUp[scSpermSeq[ithSperm].viNodeseq.len] = snpIndex
+ else:
+ let preVNode = scSpermSeq[ithSperm].viNodeseq[high(scSpermSeq[ithSperm].viNodeseq)]
+ var ltransProb = math.ln(getTrans(preVNode.pos,int(rec.POS),cmPmb=cmPmb))
+ var lnoTransProb = math.ln(1-getTrans(preVNode.pos,int(rec.POS),cmPmb=cmPmb))
+ var currentViNode = ViNode()
+ # ref/alt -> ref
+ var refTref = preVNode.pathScore[stateRef] + lnoTransProb
+ var altTref = preVNode.pathScore[stateAlt] + ltransProb
+ if refTref > altTref:
+ currentViNode.pathScore[stateRef] = refTref
+ currentViNode.pathState[stateRef] = stateRef
+ else:
+ currentViNode.pathScore[stateRef] = altTref
+ currentViNode.pathState[stateRef] = stateAlt
+ # ref/alt -> alt
+ var refTalt = preVNode.pathScore[stateRef] + ltransProb
+ var altTalt = preVNode.pathScore[stateAlt] + lnoTransProb
+
+ if refTalt > altTalt:
+ currentViNode.pathScore[stateAlt] = refTalt
+ currentViNode.pathState[stateAlt] = stateRef
+ else:
+ currentViNode.pathScore[stateAlt] = altTalt
+ currentViNode.pathState[stateAlt] = stateAlt
+ currentViNode.pathScore[stateAlt] += emissionArray[stateAlt]
+ currentViNode.pathScore[stateRef] += emissionArray[stateRef]
+ currentViNode.cAlt = int(ac.cAlt)
+ currentViNode.cRef = int(ac.cRef)
+ currentViNode.pos = int(rec.POS)
+ scSpermSeq[ithSperm].viNodeseq.add(currentViNode)
+ scSpermSeq[ithSperm].snpIndexLookUp[snpIndex] = scSpermSeq[ithSperm].viNodeseq.len
+ scSpermSeq[ithSperm].spermSnpIndexLookUp[scSpermSeq[ithSperm].viNodeseq.len] = snpIndex
+ return 0
+# The size line
\ No newline at end of file
diff --git a/src/private/utils.nim b/src/private/utils.nim
new file mode 100755
index 0000000..3d5eb4f
--- /dev/null
+++ b/src/private/utils.nim
@@ -0,0 +1,108 @@
+
+from distributions/rmath import dbinom
+import math
+import tables
+import hts
+
+type
+ allele_expr* = ref object
+ cref*: int
+ calt*: int
+ ViState* = enum
+ stateRef, stateAlt, stateN
+ ViNode* = object
+ pos*: int
+ cRef*: int
+ cAlt*: int
+ pathScore*: array[stateRef..stateAlt, float]
+ pathState*: array[stateRef..stateAlt, ViState]
+ state*: ViState
+
+# proc cref*(a:allele_expr):int = a.cref
+# proc calt*(a:allele_expr):int = a.calt
+
+proc inc_count_cref*(a:allele_expr) = inc(a.cref)
+proc inc_count_calt*(a:allele_expr) = inc(a.calt)
+# proc pathScore*(v:ViNode):array[stateRef..stateAlt, float] = v.pathScore
+
+proc getEmission*(thetaRef=0.1,thetaAlt=0.9,
+ cRef:int,cAlt:int): array[stateRef..stateAlt, float] =
+
+ var emissionScore = [dbinom(x=float(cAlt),size=(cRef+cAlt),prob=thetaRef,log=true),
+ dbinom(x=float(cAlt),size=(cRef+cAlt),prob=thetaAlt,log=true)]
+ return emissionScore
+
+proc getTrans*(pos1:int64,pos2:int64,cmPmb=0.1): float =
+ if pos2<pos1:
+ quit "Wrong order of snps"
+ var rec = 1-math.exp(-float(pos2-pos1)*1e-8*cmPmb) # for autosomes 1*cmPbm cM per Mb
+ return rec
+ #
+proc countAllele*(rec:Variant, ibam:Bam, maxTotalReads:int,
+ minTotalReads:int,
+ chrom:string, mapq: int,
+ barcodeTable:OrderedTableRef,minbsq:int,bulkBam:bool,barcodeTag:string): Table[string,allele_expr] =
+ var alleleCountTable = initTable[string,allele_expr]()
+ var rec_alt:char
+ var total_reads=0
+ rec_alt = rec.ALT[0][0]
+ for aln in ibam.query(chrom = chrom,start = rec.POS.cint-1, stop = rec.POS.cint):
+ var cbt = tag[string](aln, barcodeTag)
+ var currentCB: string
+ if cbt.isNone:
+ # echo "no cb "
+ if not bulkBam:
+ continue
+ else:
+ currentCB = "bulk"
+ else:
+ currentCB = cbt.get
+ if aln.flag.unmapped or aln.mapping_quality.cint < mapq or aln.flag.dup: continue
+ ## skip unmapped, duplicated, mapq low reads or aln.flag.secondary or aln.flag.supplementary
+ ## if not aln.flag.proper_pair: continue
+ if not barcodeTable.hasKey(currentCB):
+ continue
+ var
+ off = aln.start.int
+ qoff = 0
+ roff_only = 0
+ base = 'n'
+ position = rec.POS.cint
+ over = 0
+ for event in aln.cigar:
+ var cons = event.consumes
+ #echo $cons
+ if cons.query:
+ qoff+=event.len ## the offs to the query sequences
+ if cons.reference:
+ off += event.len ## the offs to the reference sequences
+ if not cons.query:
+ roff_only += event.len
+ if off <= position:
+ continue
+ over = off - position
+ # get the base
+ base = aln.base_at(qoff - over-1)
+ break
+ if aln.base_quality_at(qoff - over-1).cint < minbsq:
+ continue
+ total_reads+=1
+ if alleleCountTable.hasKey(currentCB):
+ if aln.base_at(qoff - over-1) == rec.REF[0]:
+ alleleCountTable[currentCB].inc_count_cref
+ continue
+ if aln.base_at(qoff - over-1) == rec_alt:
+ alleleCountTable[currentCB].inc_count_calt
+ continue
+ else:
+ var new_snp = allele_expr(cref:0,calt:0)
+ alleleCountTable[currentCB] = new_snp
+ if aln.base_at(qoff - over-1) == rec.REF[0]:
+ alleleCountTable[currentCB].inc_count_cref
+ continue
+ if aln.base_at(qoff - over-1) == rec_alt:
+ alleleCountTable[currentCB].inc_count_calt
+ continue
+ if total_reads > maxTotalReads or total_reads < minTotalReads:
+ return initTable[string,allele_expr]()
+ return alleleCountTable
\ No newline at end of file
diff --git a/src/sscocaller.nim b/src/sscocaller.nim
index 83d7b2a..6f2fb95 100755
--- a/src/sscocaller.nim
+++ b/src/sscocaller.nim
@@ -12,123 +12,17 @@ import strutils
import hts
import tables
import sequtils
+import private/utils
+
import math
-from distributions/rmath import dbinom
import streams
+import private/graph
+import private/findpath
-type
- allele_expr = ref object
- cref: int
- calt: int
-type
- # Nucleotide = enum
- # A, C, T, G
- ViState = enum
- stateRef, stateAlt, stateN
- ViNode = object
- pos: int
- cRef: int
- cAlt: int
- pathScore: array[stateRef..stateAlt, float]
- pathState: array[stateRef..stateAlt, ViState]
- state: ViState
- SpermViNodes = object
- viNodeseq: seq[ViNode]
- ## look up from SNPIndex to current Sperm SNP index
- snpIndexLookUp: Table[int,int]
- ## look up from current Sperm SNP index to SNPIndex
- spermSnpIndexLookUp: Table[int,int]
- SeqSpermViNodes = seq[SpermViNodes]
-
-proc inc_count_cref(a:allele_expr) = inc(a.cref)
-proc inc_count_calt(a:allele_expr) = inc(a.calt)
-
-proc getEmission(thetaRef=0.1,thetaAlt=0.9,
- cRef:int,cAlt:int): array[stateRef..stateAlt, float] =
-
- var emissionScore = [dbinom(x=float(cAlt),size=(cRef+cAlt),prob=thetaRef,log=true),
- dbinom(x=float(cAlt),size=(cRef+cAlt),prob=thetaAlt,log=true)]
- return emissionScore
-
-proc getTrans(pos1:int64,pos2:int64,cmPmb=0.1): float =
- if pos2<pos1:
- quit "Wrong order of snps"
- var rec = 1-math.exp(-float(pos2-pos1)*1e-8*cmPmb) # for autosomes 1*cmPbm cM per Mb
- return rec
- #
-proc countAllele(rec:Variant, ibam:Bam, maxTotalReads:int,
- minTotalReads:int,
- chrom:string, mapq: int,
- barcodeTable:OrderedTableRef,minbsq:int,bulkBam:bool,barcodeTag:string): Table[string,allele_expr] =
- var alleleCountTable = initTable[string,allele_expr]()
- var rec_alt:char
- var total_reads=0
- rec_alt = rec.ALT[0][0]
- for aln in ibam.query(chrom = chrom,start = rec.POS.cint-1, stop = rec.POS.cint):
- var cbt = tag[string](aln, barcodeTag)
- var currentCB: string
- if cbt.isNone:
- # echo "no cb "
- if not bulkBam:
- continue
- else:
- currentCB = "bulk"
- else:
- currentCB = cbt.get
- if aln.flag.unmapped or aln.mapping_quality.cint < mapq or aln.flag.dup: continue
- ## skip unmapped, duplicated, mapq low reads or aln.flag.secondary or aln.flag.supplementary
- ## if not aln.flag.proper_pair: continue
- if not barcodeTable.hasKey(currentCB):
- continue
- var
- off = aln.start.int
- qoff = 0
- roff_only = 0
- base = 'n'
- position = rec.POS.cint
- over = 0
- for event in aln.cigar:
- var cons = event.consumes
- #echo $cons
- if cons.query:
- qoff+=event.len ## the offs to the query sequences
- if cons.reference:
- off += event.len ## the offs to the reference sequences
- if not cons.query:
- roff_only += event.len
- if off <= position:
- continue
- over = off - position
- # get the base
- base = aln.base_at(qoff - over-1)
- break
- if aln.base_quality_at(qoff - over-1).cint < minbsq:
- continue
- total_reads+=1
- if alleleCountTable.hasKey(currentCB):
- if aln.base_at(qoff - over-1) == rec.REF[0]:
- alleleCountTable[currentCB].inc_count_cref
- continue
- if aln.base_at(qoff - over-1) == rec_alt:
- alleleCountTable[currentCB].inc_count_calt
- continue
- else:
- var new_snp = allele_expr(cref:0,calt:0)
- alleleCountTable[currentCB] = new_snp
- if aln.base_at(qoff - over-1) == rec.REF[0]:
- alleleCountTable[currentCB].inc_count_cref
- continue
- if aln.base_at(qoff - over-1) == rec_alt:
- alleleCountTable[currentCB].inc_count_calt
- continue
- if total_reads > maxTotalReads or total_reads < minTotalReads:
- return initTable[string,allele_expr]()
- return alleleCountTable
proc sscocaller(threads:int, vcff:string, barcodeFile:string,
bamfile:string, out_dir:string, mapq:int,
minbsq:int, mintotal:int, maxtotal:int, mindp:int, maxdp:int,
thetaREF:float, thetaALT:float, cmPmb:float,s_Chrs:seq,barcodeTag:string): int =
-
var
ibam:Bam
ivcf:VCF
@@ -167,12 +61,8 @@ proc sscocaller(threads:int, vcff:string, barcodeFile:string,
var scSpermSeq:SeqSpermViNodes
## matches with the order in barcodeTable
scSpermSeq.setLen(barcodeTable.len)
- var outFileSNPanno:FileStream
- var outFileTotalCountMtx:FileStream
- var outFileAltCountMtx:FileStream
- # var outHeaderMtx:FileStream
- var outFileVStateMtx:FileStream
- var viSegmentInfo: FileStream
+ var outFileSNPanno,outFileTotalCountMtx,outFileAltCountMtx,outFileVStateMtx,viSegmentInfo:FileStream
+
try:
outFileSNPanno = openFileStream(out_dir & chrom & "_snpAnnot.txt", fmWrite)
outFileTotalCountMtx = openFileStream(out_dir & chrom & "_totalCount.mtx", fmWrite)
@@ -190,20 +80,14 @@ proc sscocaller(threads:int, vcff:string, barcodeFile:string,
outFileAltCountMtx.writeLine(' '.repeat(50))
outFileVStateMtx.writeLine("%%MatrixMarket matrix coordinate integer general")
outFileVStateMtx.writeLine(' '.repeat(50))
-
outFileSNPanno.writeLine("POS" & "\t" & "REF" & "\t" & "ALT" )
+
for rec in ivcf.query(chrom):
if rec.ALT.len > 1: continue
if rec.ALT.len == 0: continue
## alleleCountTable contains for this SNP.POS, each cell barcode's allele counts
- var alleleCountTable = countAllele(rec=rec, ibam=ibam,
- chrom=chrom, mapq=mapq,
- barcodeTable=barcodeTable,
- minbsq=minbsq,
- maxTotalReads = maxtotal,
- minTotalReads = mintotal,
- bulkBam = bulkBam,
- barcodeTag = barcodeTag)
+ var alleleCountTable = countAllele(rec=rec, ibam=ibam, chrom=chrom, mapq=mapq, barcodeTable=barcodeTable,minbsq=minbsq,
+ maxTotalReads = maxtotal, minTotalReads = mintotal,bulkBam = bulkBam, barcodeTag = barcodeTag)
if alleleCountTable.len==0: continue
var rec_alt:char
@@ -212,82 +96,24 @@ proc sscocaller(threads:int, vcff:string, barcodeFile:string,
## add to snpAnnoSeq, later write to SNPannot file, which contains SNP.pos, SNP.ref,SNP.alt; The rowAnnotations
snpIndex += 1
outFileSNPanno.writeLine($rec.POS & "\t" & $rec.REF[0] & "\t" & $rec_alt )
- for bc, ac in alleleCountTable.mpairs:
- # ac.tostring(acs)
- ## mindp, maxdp, they are values per cell
- if (ac.cref+ac.calt) <= mindp or (ac.cref+ac.calt) >= maxdp: continue
- var ithSperm = barcodeTable[bc]
- ## write to mtx Ref count
- outFileTotalCountMtx.writeLine($snpIndex & " " & $(ithSperm+1) & " " & $(ac.cRef+ac.cAlt))
- outFileAltCountMtx.writeLine($snpIndex & " " & $(ithSperm+1) & " " & $ac.cAlt)
- nnsize += 1
- var emissionArray = getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,cRef=ac.cRef,cAlt=ac.cAlt)
- if scSpermSeq[ithSperm].viNodeseq.len==0:
- var currentViNode = ViNode()
- currentViNode.pathScore[stateRef] = math.ln(initProb[stateRef])+emissionArray[stateRef]
- currentViNode.pathScore[stateAlt] = math.ln(initProb[stateAlt])+emissionArray[stateAlt]
- currentViNode.pathState[stateRef] = stateN
- currentViNode.pathState[stateAlt] = stateN
- currentViNode.state = stateN
- currentViNode.pos = int(rec.POS)
- currentViNode.cAlt = int(ac.cAlt)
- currentViNode.cRef = int(ac.cRef)
-
- scSpermSeq[ithSperm].viNodeseq.add(currentViNode)
- scSpermSeq[ithSperm].snpIndexLookUp[snpIndex] = scSpermSeq[ithSperm].viNodeseq.len
- scSpermSeq[ithSperm].spermSnpIndexLookUp[scSpermSeq[ithSperm].viNodeseq.len] = snpIndex
- else:
- let preVNode = scSpermSeq[ithSperm].viNodeseq[high(scSpermSeq[ithSperm].viNodeseq)]
- var ltransProb = math.ln(getTrans(preVNode.pos,int(rec.POS),cmPmb=cmPmb))
- var lnoTransProb = math.ln(1-getTrans(preVNode.pos,int(rec.POS),cmPmb=cmPmb))
- var currentViNode = ViNode()
- # ref/alt -> ref
- var refTref = preVNode.pathScore[stateRef] + lnoTransProb
- var altTref = preVNode.pathScore[stateAlt] + ltransProb
- if refTref > altTref:
- currentViNode.pathScore[stateRef] = refTref
- currentViNode.pathState[stateRef] = stateRef
- else:
- currentViNode.pathScore[stateRef] = altTref
- currentViNode.pathState[stateRef] = stateAlt
- # ref/alt -> alt
- var refTalt = preVNode.pathScore[stateRef] + ltransProb
- var altTalt = preVNode.pathScore[stateAlt] + lnoTransProb
-
- if refTalt > altTalt:
- currentViNode.pathScore[stateAlt] = refTalt
- currentViNode.pathState[stateAlt] = stateRef
- else:
- currentViNode.pathScore[stateAlt] = altTalt
- currentViNode.pathState[stateAlt] = stateAlt
- currentViNode.pathScore[stateAlt] += emissionArray[stateAlt]
- currentViNode.pathScore[stateRef] += emissionArray[stateRef]
- currentViNode.cAlt = int(ac.cAlt)
- currentViNode.cRef = int(ac.cRef)
- currentViNode.pos = int(rec.POS)
- scSpermSeq[ithSperm].viNodeseq.add(currentViNode)
- scSpermSeq[ithSperm].snpIndexLookUp[snpIndex] = scSpermSeq[ithSperm].viNodeseq.len
- scSpermSeq[ithSperm].spermSnpIndexLookUp[scSpermSeq[ithSperm].viNodeseq.len] = snpIndex
- # The size line
-
- var transitFlag = false
- var cSNP = 0
- var posEnd,posStart:int64
- var inferProb,reverseProb,transProb = 0.0
- var currentEm,prevEm: array[stateRef..stateAlt, float]
+ discard addViNode(barcodeTable = barcodeTable, alleleCountTable = alleleCountTable, scSpermSeq = scSpermSeq,
+ outFileTotalCountMtx = outFileTotalCountMtx, outFileAltCountMtx = outFileAltCountMtx, nnsize = nnsize,
+ mindp = mindp, maxdp = maxdp, thetaRef = thetaRef, thetaAlt = thetaAlt, snpIndex = snpIndex, rec=rec,
+ initProb = initProb, cmPmb = cmPmb)
+ var posEnd: int64
+ var inferProb,reverseProb = 0.0
+ var currentEm: array[stateRef..stateAlt, float]
var lastNode: ViNode
var spermVNseq: SpermViNodes
var ithSNP: int
## trans/no trans
- var rightGap,leftGap: array[0..1, float]
+
for ithSperm in 0..(scSpermSeq.len-1):
## rightGap,leftGap = [0.0,0.0]
spermVNseq = scSpermSeq[ithSperm]
if spermVNseq.viNodeseq.len==0: continue
lastNode = spermVNseq.viNodeseq[high(spermVNseq.viNodeseq)]
- currentEm = getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,
- cRef=lastNode.cRef,
- cAlt=lastNode.cAlt)
+ currentEm = getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,cRef=lastNode.cRef, cAlt=lastNode.cAlt)
if lastNode.pathScore[stateRef] > lastNode.pathScore[stateAlt]:
scSpermSeq[ithSperm].viNodeseq[high(scSpermSeq[ithSperm].viNodeseq)].state = stateRef
ithSNP = scSpermSeq[ithSperm].spermSnpIndexLookUp[high(scSpermSeq[ithSperm].viNodeseq)+1]
@@ -301,90 +127,13 @@ proc sscocaller(threads:int, vcff:string, barcodeFile:string,
inferProb = currentEm[stateAlt]
reverseProb = currentEm[stateRef]
posEnd = lastNode.pos
- cSNP = 1
- ## traceback for yielding the most probable state sequence
- for i in 1..high(scSpermSeq[ithSperm].viNodeseq):
- var state = scSpermSeq[ithSperm].viNodeseq[^i].state
- scSpermSeq[ithSperm].viNodeseq[^(i+1)].state = scSpermSeq[ithSperm].viNodeseq[^i].pathState[state]
- prevEm = getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,
- cRef=scSpermSeq[ithSperm].viNodeseq[^(i+1)].cRef,
- cAlt=scSpermSeq[ithSperm].viNodeseq[^(i+1)].cAlt)
- ithSNP = scSpermSeq[ithSperm].spermSnpIndexLookUp[high(scSpermSeq[ithSperm].viNodeseq)-i+1]
- transProb = getTrans(scSpermSeq[ithSperm].viNodeseq[^(i+1)].pos,
- scSpermSeq[ithSperm].viNodeseq[^(i)].pos,
- cmPmb=cmPmb)
- if scSpermSeq[ithSperm].viNodeseq[^(i+1)].state == stateRef:
- outFileVStateMtx.writeLine($ithSNP & " " & $(ithSperm+1) & " 1")
- if state == stateRef:
- # not transitioning to a different state ie still in this segment of same state
- inferProb+=prevEm[stateRef]
- reverseProb+=prevEm[stateAlt]
- cSNP += 1
- transitFlag = false
- #posStart = scSpermSeq[ithSperm].viNodeseq[^(i+1)].pos
- else: # there is transition to different state: ref(start) to alt(end) now output the segment info
- posStart = scSpermSeq[ithSperm].viNodeseq[^(i)].pos
- #leftGapSize = scSpermSeq[ithSperm].viNodeseq[^(i)].pos - scSpermSeq[ithSperm].viNodeseq[^(i+1)].pos
- leftGap=[math.ln(transProb),math.ln(1-transProb)]
- inferProb+=leftGap[0]
- reverseProb+=leftGap[1]
- viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 2")
- transitFlag = true
- cSNP = 1
- rightGap = leftGap
- inferProb = prevEm[stateRef]+rightGap[0]
- reverseProb = prevEm[stateAlt]+rightGap[1]
- posEnd = scSpermSeq[ithSperm].viNodeseq[^(i+1)].pos
- else:
- outFileVStateMtx.writeLine($ithSNP & " " & $(ithSperm+1) & " 2")
- if state == stateAlt:
- # not transitioning to a different state ie still in this segment of same state
- inferProb += prevEm[stateAlt]
- reverseProb += prevEm[stateRef]
- cSNP += 1
- transitFlag = false
- else:
- ## state transit
- posStart = scSpermSeq[ithSperm].viNodeseq[^(i)].pos
- leftGap=[math.ln(transProb),math.ln(1-transProb)]
- inferProb += leftGap[0]
- reverseProb += leftGap[1]
- viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 1" )
- transitFlag = true
- cSNP = 1
- rightGap = leftGap
- inferProb = prevEm[stateAlt]+rightGap[0]
- reverseProb = prevEm[stateRef]+rightGap[1]
- posEnd = scSpermSeq[ithSperm].viNodeseq[^(i+1)].pos
- ## traced to the start position of the chromosome for this cell
- #leftGap = [0.0,0.0]
- if not transitFlag:
- ## the first SNP is included in the segment from traced from back
- posStart = scSpermSeq[ithSperm].viNodeseq[0].pos
- if scSpermSeq[ithSperm].viNodeseq[0].state == stateRef:
- viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 1" )
- else:
- viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 2" )
- else:
- ## the first node has different state from the second, the first node has its own segment
- posStart = scSpermSeq[ithSperm].viNodeseq[0].pos
- posEnd = posStart
- cSNP = 1
- currentEm = getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,
- cRef=scSpermSeq[ithSperm].viNodeseq[0].cRef,
- cAlt=scSpermSeq[ithSperm].viNodeseq[0].cAlt)
- transProb = getTrans(scSpermSeq[ithSperm].viNodeseq[0].pos,
- scSpermSeq[ithSperm].viNodeseq[1].pos,
- cmPmb=cmPmb)
- if scSpermSeq[ithSperm].viNodeseq[0].state == stateRef:
- inferProb = currentEm[stateRef]+math.ln(transProb)
- reverseProb = currentEm[stateAlt]+math.ln(1-transProb)
- viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 1" )
- else:
- inferProb = currentEm[stateAlt]+math.ln(transProb)
- reverseProb = currentEm[stateRef]+math.ln(1-transProb)
- viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 2" )
- transitFlag = false
+ ## call pathTrackBack will write the most probably hidden state seq and viterbi segment info to the
+ ## relevant File Streams.
+
+ discard pathTrackBack(currentSperm = scSpermSeq[ithSperm], ithSperm = ithSperm, thetaRef = thetaRef,
+ thetaAlt = thetaAlt, cmPmb = cmPmb,outFileVStateMtx = outFileVStateMtx,
+ viSegmentInfo = viSegmentInfo, posEnd = posEnd, inferProb = inferProb,reverseProb = reverseProb)
+
outFileTotalCountMtx.setPosition(49)
outFileVStateMtx.setPosition(49)
outFileAltCountMtx.setPosition(49)
@@ -401,11 +150,10 @@ proc sscocaller(threads:int, vcff:string, barcodeFile:string,
viSegmentInfo.close()
ibam.close()
ivcf.close()
-
return 0
when(isMainModule):
- let version = "0.2.1"
+ let version = "0.2.2"
var doc = format("""
$version
@@ -424,19 +172,19 @@ Arguments:
Options:
- -t --threads <threads> number of BAM decompression threads [default: 4]
- -cb --cellbarcode <cellbarcode> the cell barcode tag, by default it is CB
- -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20]
+ -t --threads <threads> number of BAM decompression threads [default: 4]
+ -cb --cellbarcode <cellbarcode> the cell barcode tag, by default it is CB
+ -MQ --minMAPQ <mapq> Minimum MAPQ for read filtering [default: 20]
-BQ --baseq <baseq> base quality threshold for a base to be used for counting [default: 13]
- -CHR --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms)
- -minDP --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1]
- -maxDP --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 5]
- -maxTotalDP --maxTotalDP <maxTotalDP> the maximum DP across all barcodes for a SNP to be included in the output file [default: 25]
- -minTotalDP --minTotalDP <minTotalDP> the minimum DP across all barcodes for a SNP to be included in the output file [default: 10]
- -chrName --chrName <chrName> the chr names with chr prefix or not, if not supplied then no prefix
- -thetaREF --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1]
- -thetaALT --thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9]
- -cmPmb --cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default 0.1]
+ -CHR --chrom <chrom> the selected chromsome (whole genome if not supplied,separate by comma if multiple chroms)
+ -minDP --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1]
+ -maxDP --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 5]
+ -maxTotalDP --maxTotalDP <maxTotalDP> the maximum DP across all barcodes for a SNP to be included in the output file [default: 30]
+ -minTotalDP --minTotalDP <minTotalDP> the minimum DP across all barcodes for a SNP to be included in the output file [default: 10]
+ -chrName --chrName the chr names with chr prefix or not, if not supplied then no prefix
+ -thetaREF --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1]
+ -thetaALT --thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9]
+ -cmPmb --cmPmb <cmPmb> the average centiMorgan distances per megabases default 0.1 cm per Mb [default 0.1]
-h --help show help
Examples
@@ -462,65 +210,27 @@ Options:
thetaALT:float
cmPmb:float
barcodeTag="CB"
+ threads = parse_int($args["--threads"])
+ barcodeTag = $args["--barcodeTag"]
+ mindp = parse_int($args["--minDP"])
+ maxdp = parse_int($args["--maxDP"])
+ maxtotal = parse_int($args["--maxTotalDP"])
+ mintotal = parse_int($args["--minTotalDP"])
+ bamfile = $args["<BAM>"]
+ barcodeFile = $args["<barcodeFile>"]
+ out_dir = $args["<out_prefix>"]
+ vcff = $args["<VCF>"]
+ mapq = parse_int($args["--minMAPQ"])
+ minbsq = parse_int($args["--baseq"])
+ thetaRef = parse_float($args["--thetaREF"])
+ thetaAlt = parse_float($args["--thetaALT"])
+ cmPmb = parse_float($args["--cmPmb"])
- if($args["--threads"] != "nil"):
- threads = parse_int($args["--threads"])
- if($args["--cellbarcode"] != "nil"):
- barcodeTag = $args["--barcodeTag"]
- else: threads = 4
- if($args["--minDP"] != "nil"):
- mindp = parse_int($args["--minDP"])
- else: mindp = 1
- if($args["--maxDP"] != "nil"):
- maxdp = parse_int($args["--maxDP"])
- else: maxdp = 10
-
- if($args["--maxTotalDP"] != "nil"):
- maxtotal = parse_int($args["--maxTotalDP"])
- else: maxtotal = 30
-
- if($args["--minTotalDP"] != "nil"):
- mintotal = parse_int($args["--minTotalDP"])
- else: mintotal = 10
-
- if($args["<BAM>"] == "nil"):
- quit "input bam is required"
- else: bamfile = $args["<BAM>"]
-
- if($args["<barcodeFile>"] == "nil"):
- quit "input barcodeFile is required"
- else: barcodeFile = $args["<barcodeFile>"]
-
- if($args["<out_prefix>"] == "nil"):
- quit "output prefix is required"
- else: out_dir = $args["<out_prefix>"]
-
- if($args["<VCF>"] == "nil"):
- quit "input VCF file is required"
- else: vcff = $args["<VCF>"]
-
- if($args["--minMAPQ"] != "nil"):
- mapq = parse_int($args["--minMAPQ"])
- else: mapq = 20
- if($args["--baseq"] != "nil"):
- minbsq = parse_int($args["--baseq"])
- else: minbsq = 13
- if($args["--thetaREF"] != "nil"):
- thetaRef = parse_float($args["--thetaREF"])
- else: thetaRef = 0.1
-
- if($args["--thetaALT"] != "nil"):
- thetaAlt = parse_float($args["--thetaALT"])
- else: thetaAlt = 0.9
-
- if($args["--cmPmb"] != "nil"):
- cmPmb = parse_float($args["--cmPmb"])
- else: cmPmb = 0.1
if($args["--chrom"] != "nil"):
selectedChrs = $args["--chrom"]
else:
let a = toSeq(1..19)
- if($args["--chrName"] == "nil"):
+ if(not args["--chrName"]):
let b = map(a, proc (x: int): string = "" & $x)
let all_Chrs = concat(b,@["X","Y"])
selectedChrs = all_Chrs.join(",")
@@ -528,11 +238,8 @@ Options:
let b = map(a, proc (x: int): string = "chr" & $x)
let all_Chrs = concat(b,@["chrX","chrY"])
selectedChrs = all_Chrs.join(",")
-
let s_Chrs = selectedChrs.split(',')
- #echo $s_Chrs
-
- #var args = commandLineParams()
+
discard sscocaller(threads, vcff, barcodeFile, bamfile,
out_dir, mapq, minbsq, mintotal,
maxtotal, mindp, maxdp, thetaREF, thetaALT, cmPmb,s_Chrs,barcodeTag)
--
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