From 8624a9172d5f163e23f1541f84e7613792e7b548 Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Tue, 25 May 2021 15:18:51 +1000
Subject: [PATCH] add versioning and refactored code to have mainModule check
---
src/sscocaller.nim | 484 +++++++++++++++++++++++----------------------
1 file changed, 246 insertions(+), 238 deletions(-)
diff --git a/src/sscocaller.nim b/src/sscocaller.nim
index 5002669..9976b7a 100755
--- a/src/sscocaller.nim
+++ b/src/sscocaller.nim
@@ -16,141 +16,127 @@ import math
from distributions/rmath import dbinom
import streams
-#echo paramCount(), " ", paramStr(1)
+type
+ allele_expr = ref object
+ cref: int
+ calt: int
+type
+ AlleleExpr = object
+ cRef: int
+ cAlt: int
+ # 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]
+#var alexprSeq:seq[AlleleExpr]
-proc sscocaller(argv: var seq[string]): int =
- let doc = """
- Obtain allele counts for cell barcodes listed in barcodeFile at the SNP positions in VCF from the BAM file.
-
- Usage:
- sscocaller [options] <BAM> <VCF> <barcodeFile> <out_prefix>
-
- Options:
- -t --threads <threads> number of BAM decompression threads [default: 4]
- -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]
- -h --help show help
-
- Examples
- ./sscocaller --threads 10 AAAGTAGCACGTCTCT-1.raw.bam AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz barcodeFile.tsv ./percell/ccsnp-
- """
- let args = docopt(doc, argv=argv)
-
- var
- ibam:Bam
- threads:int
- vcff:string
- ivcf:VCF
- barcodeFile:string
- bamfile:string
- selectedChrs:string
- out_dir:string
- mapq:int
- minbsq:int
- mintotal:int
- maxtotal:int
- mindp:int
- maxdp:int
- thetaREF:float
- thetaALT:float
- cmPmb:float
- type
- allele_expr = ref object
- cref: int
- calt: int
-
- proc inc_count_cref(a:allele_expr) = inc(a.cref)
- proc inc_count_calt(a:allele_expr) = inc(a.calt)
- proc reset_count(a:allele_expr) =
- a.calt = 0
- a.cref = 0
-
- # proc cref(a:allele_expr): int {.inline.} = return a.cref
- # proc calt(a:allele_expr): int {.inline.} = return a.calt
-
- proc tostring(a:allele_expr, s:var string) {.inline.} =
- s.set_len(0)
- s.add("\t" & $a.cref & "," & $a.calt)
+proc inc_count_cref(a:allele_expr) = inc(a.cref)
+proc inc_count_calt(a:allele_expr) = inc(a.calt)
+proc reset_count(a:allele_expr) =
+ a.calt = 0
+ a.cref = 0
+proc tostring(a:allele_expr, s:var string) {.inline.} =
+ s.set_len(0)
+ s.add("\t" & $a.cref & "," & $a.calt)
+proc getEmission(thetaRef=0.1,thetaAlt=0.9,
+ cRef:int,cAlt:int): array[stateRef..stateAlt, float] =
- if($args["--threads"] != "nil"):
- threads = parse_int($args["--threads"])
- else: threads = 4
- if($args["--minDP"] != "nil"):
- mindp = parse_int($args["--minDP"])
- else: mindp = 1
- if($args["--maxDP"] != "nil"):
- maxdp = parse_int($args["--maxDP"])
- else: maxdp = 10
+ var emissionScore = [dbinom(x=float(cAlt),size=(cRef+cAlt),prob=thetaRef,log=true),
+ dbinom(x=float(cAlt),size=(cRef+cAlt),prob=thetaAlt,log=true)]
+ return emissionScore
- if($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 = $args["<VCF>"]
+proc getTrans(pos1:int64,pos2:int64,cmPmb=0.1): float =
+ if pos2<pos1:
+ quit "Wrong order of snps"
+ var rec = 1-math.exp(-float(pos2-pos1)*1e-8*cmPmb) # for autosomes 1*cmPbm cM per Mb
+ return rec
+ #
+proc countAllele(rec:Variant, ibam:Bam, maxTotalReads:int,
+ minTotalReads:int,
+ chrom:string, mapq: int,
+ barcodeTable:OrderedTableRef,minbsq:int): Table[string,allele_expr] =
+ var alleleCountTable = initTable[string,allele_expr]()
+ var rec_alt:char
+ var total_reads=0
+ rec_alt = rec.ALT[0][0]
+ for aln in ibam.query(chrom = chrom,start = rec.POS.cint-1, stop = rec.POS.cint):
+ var cbt = tag[string](aln, "CB")
+ if cbt.isNone:
+ # echo "no cb "
+ continue
+ if aln.flag.unmapped or aln.mapping_quality.cint < mapq or aln.flag.dup: continue
+ ## skip unmapped, duplicated, mapq low reads or aln.flag.secondary or aln.flag.supplementary
+ ## if not aln.flag.proper_pair: continue
- if($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 not barcodeTable.hasKey(cbt.get):
+ 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 $cons
+ if cons.query:
+ qoff+=event.len ## the offs to the query sequences
+ if cons.reference:
+ off += event.len ## the offs to the reference sequences
+ if not cons.query:
+ roff_only += event.len
+ if off <= position:
+ continue
+ over = off - position
+ # get the base
+ base = aln.base_at(qoff - over-1)
+ break
+ if aln.base_quality_at(qoff - over-1).cint < minbsq:
+ continue
+ total_reads+=1
+ if alleleCountTable.hasKey(cbt.get):
+ if aln.base_at(qoff - over-1) == rec.REF[0]:
+ alleleCountTable[cbt.get].inc_count_cref
+ continue
+ if aln.base_at(qoff - over-1) == rec_alt:
+ alleleCountTable[cbt.get].inc_count_calt
+ continue
+ else:
+ var new_snp = allele_expr(cref:0,calt:0)
+ alleleCountTable[cbt.get] = new_snp
+ if aln.base_at(qoff - over-1) == rec.REF[0]:
+ alleleCountTable[cbt.get].inc_count_cref
+ continue
+ if aln.base_at(qoff - over-1) == rec_alt:
+ alleleCountTable[cbt.get].inc_count_calt
+ continue
+ if total_reads > maxTotalReads or total_reads < minTotalReads:
+ return initTable[string,allele_expr]()
+ return alleleCountTable
+proc sscocaller(threads:int, vcff:string, barcodeFile:string,
+ bamfile:string, out_dir:string, mapq:int,
+ minbsq:int, mintotal:int, maxtotal:int, mindp:int, maxdp:int,
+ thetaREF:float, thetaALT:float, cmPmb:float,s_Chrs:seq): int =
- if($args["--thetaALT"] != "nil"):
- thetaAlt = parse_float($args["--thetaALT"])
- else: thetaAlt = 0.9
-
- if($args["--cmPmb"] != "nil"):
- cmPmb = parse_float($args["--cmPmb"])
- else: cmPmb = 0.1
-
- echo "min mapq ", mapq, " min base qual ", minbsq
-
- if($args["--chrom"] != "nil"):
- selectedChrs = $args["--chrom"]
- else:
- let a = toSeq(1..19)
- if($args["--chrName"] == "nil"):
- let b = map(a, proc (x: int): string = "" & $x)
- let all_Chrs = concat(b,@["X","Y"])
- selectedChrs = all_Chrs.join(",")
- else:
- 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
+ ibam:Bam
+ ivcf:VCF
if not open(ibam, bamfile, threads=threads, index = true):
quit "couldn't open input bam"
if not open(ivcf, vcff, threads=threads):
@@ -170,107 +156,9 @@ proc sscocaller(argv: var seq[string]): int =
if $kstr.s[0] == "#":
continue
var v = $kstr.s
- ## barcodekey:spermIndex pair
discard barcodeTable.hasKeyOrPut(v, ithSperm)
- ithSperm+=1
- echo "fetch given SNPs in ", barcodeTable.len ," single cells"
-
- type
- AlleleExpr = object
- cRef: int
- cAlt: int
- # 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]
-
+ ithSperm+=1
let initProb:array[stateRef..stateAlt, float]=[0.5,0.5]
- var alexprSeq:seq[AlleleExpr]
- 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
-
- #echo getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,cRef=10,cAlt=0)
-
- 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): 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):
- 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
- var cbt = tag[string](aln, "CB")
- if cbt.isNone: continue
- if not barcodeTable.hasKey(cbt.get): 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
- 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(cbt.get):
- if aln.base_at(qoff - over-1) == rec.REF[0]:
- alleleCountTable[cbt.get].inc_count_cref
- continue
- if aln.base_at(qoff - over-1) == rec_alt:
- alleleCountTable[cbt.get].inc_count_calt
- continue
- else:
- var new_snp = allele_expr(cref:0,calt:0)
- alleleCountTable[cbt.get] = new_snp
- if aln.base_at(qoff - over-1) == rec.REF[0]:
- alleleCountTable[cbt.get].inc_count_cref
- continue
- if aln.base_at(qoff - over-1) == rec_alt:
- alleleCountTable[cbt.get].inc_count_calt
- continue
- if total_reads > maxTotalReads or total_reads < minTotalReads:
- return initTable[string,allele_expr]()
- return alleleCountTable
-
## iterate through each selected chromosome
for chrom in s_Chrs:
# var scTable = initTable[string,SingleSpermRec]()
@@ -278,8 +166,7 @@ proc sscocaller(argv: var seq[string]): int =
var spermIndex = 0
## number of non zeros
var nnsize = 0
-# var snpAnnoSeq:seq[SNPAnnot]
- var scSpermSeq:seq[SpermViNodes]
+ var scSpermSeq:SeqSpermViNodes
## matches with the order in barcodeTable
scSpermSeq.setLen(barcodeTable.len)
var outFileSNPanno:FileStream
@@ -338,7 +225,6 @@ proc sscocaller(argv: var seq[string]): int =
nnsize += 1
var emissionArray = getEmission(thetaRef=thetaRef,thetaAlt=thetaAlt,cRef=ac.cRef,cAlt=ac.cAlt)
if scSpermSeq[ithSperm].viNodeseq.len==0:
- echo "first node to ", ithSperm
var currentViNode = ViNode()
currentViNode.pathScore[stateRef] = math.ln(initProb[stateRef])+emissionArray[stateRef]
currentViNode.pathScore[stateAlt] = math.ln(initProb[stateAlt])+emissionArray[stateAlt]
@@ -353,7 +239,6 @@ proc sscocaller(argv: var seq[string]): int =
scSpermSeq[ithSperm].snpIndexLookUp[snpIndex] = scSpermSeq[ithSperm].viNodeseq.len
scSpermSeq[ithSperm].spermSnpIndexLookUp[scSpermSeq[ithSperm].viNodeseq.len] = snpIndex
else:
- #echo "additional node to a cell"
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))
@@ -430,8 +315,6 @@ proc sscocaller(argv: var seq[string]): int =
transProb = getTrans(scSpermSeq[ithSperm].viNodeseq[^(i+1)].pos,
scSpermSeq[ithSperm].viNodeseq[^(i)].pos,
cmPmb=cmPmb)
- # echo inferProb
- # echo reverseProb
if scSpermSeq[ithSperm].viNodeseq[^(i+1)].state == stateRef:
outFileVStateMtx.writeLine($ithSNP & " " & $(ithSperm+1) & " 1")
if state == stateRef:
@@ -448,8 +331,6 @@ proc sscocaller(argv: var seq[string]): int =
inferProb+=leftGap[0]
reverseProb+=leftGap[1]
viSegmentInfo.writeLine("ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(inferProb-reverseProb) & " " & $cSNP & " 2")
- #echo "ithSperm" & $ithSperm & " " & $posStart & " " & $posEnd & " " & $(reverseProb/inferProb) & " " & $cSNP
- #echo $(inferProb/reverseProb)
transitFlag = true
cSNP = 1
rightGap = leftGap
@@ -524,6 +405,133 @@ proc sscocaller(argv: var seq[string]): int =
ivcf.close()
return 0
+
+when(isMainModule):
+ let version = "0.1.0"
+ var doc = format("""
+ $version
+
+ Usage:
+ sscocaller [options] <BAM> <VCF> <barcodeFile> <out_prefix>
+
+Arguments:
+
+ <BAM> the read alignment file with records of single-cell DNA reads
+
+ <VCF> the variant call file with records of SNPs
+
+ <barcodeFile> the text file containing the list of cell barcodes
+
+ <out_prefix> the prefix of output files
+
+
+Options:
+ -t --threads <threads> number of BAM decompression threads [default: 4]
+ -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]
+ -h --help show help
+
+ Examples
+ ./sscocaller --threads 10 AAAGTAGCACGTCTCT-1.raw.bam AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz barcodeFile.tsv ./percell/ccsnp-
+""" % ["version", version])
+
+ let args = docopt(doc, version=version)
+
+ var
+ threads:int
+ vcff:string
+ barcodeFile:string
+ bamfile:string
+ selectedChrs:string
+ out_dir:string
+ mapq:int
+ minbsq:int
+ mintotal:int
+ maxtotal:int
+ mindp:int
+ maxdp:int
+ thetaREF:float
+ thetaALT:float
+ cmPmb:float
+
+ if($args["--threads"] != "nil"):
+ threads = parse_int($args["--threads"])
+ else: threads = 4
+ if($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"):
+ let b = map(a, proc (x: int): string = "" & $x)
+ let all_Chrs = concat(b,@["X","Y"])
+ selectedChrs = all_Chrs.join(",")
+ else:
+ let b = map(a, proc (x: int): string = "chr" & $x)
+ let all_Chrs = concat(b,@["chrX","chrY"])
+ selectedChrs = all_Chrs.join(",")
-var args = commandLineParams()
-discard sscocaller(args)
+ 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)
+
--
GitLab