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update pipeline for pruning #19

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update pipeline for pruning #19

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eea4e82
update pipeline for pruning
ASLeonard Mar 31, 2022
4a3026b
Fixing missed pan references
ASLeonard Apr 1, 2022
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44 changes: 35 additions & 9 deletions pipeline/GoodPanGenomeGraph.snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -284,11 +284,9 @@ done
rule GenRawGenomeGraph:
input:
TRfa = expand(outdir + "{{genome}}.{hap}.tr.fasta", hap=haps),
ILbam = lambda wildcards: [bams[wildcards.genome]] if prune else [],
mapping = outdir + "OrthoMap.v2.tsv",
output:
rawPBkmers = expand(outdir + "{{genome}}.rawPB.{kmerType}.kmers", kmerType=kmerTypes),
rawILkmers = [outdir + "{genome}.rawIL.tr.kmers"] if prune else []
resources:
cores = 24 if prune else 1,
mem = lambda wildcards, attempt: 55 + 20*(attempt-1)
Expand All @@ -312,13 +310,35 @@ cd {params.od}
module load gcc

{params.sd}/bin/vntr2kmers_thread -g -m <(cut -f $(({params.hi}+1)),$(({params.hi}+2)) {input.mapping}) -k {params.ksize} -fs {params.FS} -ntr {params.FS} -o {wildcards.genome}.rawPB -fa 2 {input.TRfa}
"""

if [ {params.prune} == "1" ]; then
rule GeneratePruningAlignments:
input:
ILbam = lambda wildcards: [bams[wildcards.genome]] if prune else [],
serials = lambda wildcards: expand(outdir + "{genome}.rawPB.{binKmerType}", genome=wildcards.genome,binKmerType=binKmerTypes)
output:
rawILkmers = outdir + "{genome}.rawIL.tr.kmers"
resources:
cores=1
params:
name = "GenRawGenomeGraph",
copts = copts,
sd = srcdir,
od = outdir,
ksize = ksize,
FS = FS,
cth = cth,
rth = rth,
rstring = rstring,
thcth = thcth,
hi = lambda wildcards: 2*genomes.index(wildcards.genome)
shell:
'''
cd {params.od}
samtools fasta -@2 -n {input.ILbam} |
{params.sd}/bin/bam2pe -fai /dev/stdin |
{params.sd}/bin/danbing-tk -g {params.thcth} -k {params.ksize} -qs {params.od}/{wildcards.genome}.rawPB -fai /dev/stdin -o {wildcards.genome}.rawIL -p {resources.cores} -cth {params.cth} -rth {params.rth}
fi
"""
'''


rule EvalRawGenomeGraph:
Expand Down Expand Up @@ -398,11 +418,17 @@ module load gcc
{params.sd}/bin/genPanKmers -o pan -m - -k {params.kmerpref}
"""

def get_filename(genome):
if genome == 'pan':
return 'pan'
else:
return f'{genome}.rawPB'

rule GenSerializedGraphAndIndex:
input:
panKmers = expand(outdir + "pan.{kmerType}.kmers", kmerType=kmerTypes)
txtKmers = expand(outdir + "{{genome}}.{kmerType}.kmers", kmerType=kmerTypes)
output:
binKmers = expand(outdir + "pan.{binKmerType}", binKmerType=binKmerTypes)
binKmers = expand(outdir + "{{genome}}.{binKmerType}", binKmerType=binKmerTypes)
resources:
cores = 2,
mem = lambda wildcards, attempt: 90+20*(attempt-1)
Expand All @@ -411,13 +437,13 @@ rule GenSerializedGraphAndIndex:
copts = copts,
sd = srcdir,
od = outdir,
pref = f"{outdir}/pan"
pref = f"{outdir}/{{wildcards.genome}}"
shell:"""
cd {params.od}
ulimit -c 20000
module load gcc

{params.sd}/bin/ktools serialize {params.pref}
{params.sd}/bin/ktools ksi pan.tr.kmers >{params.pref}.tr.ksi
{params.sd}/bin/ktools ksi {wildcards.genome}.tr.kmers >{params.pref}.tr.ksi
"""