def pipeSaklCleanReadsMito(strain, refSt):
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanPE/s_1_%s-trim_unmapped_unmapped.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanPE/s_2_%s-trim_unmapped_unmapped.fq" % (strain)
repOut = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Mito/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Mito/mito%s.fasta" % (refSt)
#ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Mito/mitoCBS5828.fasta"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
outBWA = "aln_%s_unmapped" % strain
opt = "-n 8 -o 2"
if not "Run3" in reads1:
opt += " -I"
#opt = "-n 10 -o 4"
#ficSam = traitementBWA.lanceBWA(outBWA2,lUnmappedReads[0],lUnmappedReads[1],repOut,ref,opt)
ficSam = traitementBWA.lanceBWA(outBWA, reads1, reads2, repOut, ref, opt)
#ficSam = traitementBWA.lanceBWA(outBWA,reads1,reads2,repOut,ref)
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
# renomme le fichier de mapping
ficSamAll = "%s/aln_%s_unmapped_PE.sam" % (repOut, strain)
cmdB = "mv %s %s" % (ficSamInRef, ficSamAll)
os.system(cmdB)
#traitementSamtools.lancePipeSamtools(ficSamAll,ref)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
# puis qq stats et estimation du nombre de SNP etc
ficVarFilter = traitementSamtools.lancePipeSamtoolsSansRel(ficSamAll, ref)
#ficVarFilter = traitementSamtools.lancePipeSamtools(ficSamAll,ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeSakl(strain,run):
if run == "run2":
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run2/s_3_1_%s_unmapped_unmapped.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run2/s_3_2_%s_unmapped_unmapped.fq" % (strain)
else:
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/s_8_1_%s_unmapped_unmapped.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/s_8_2_%s_unmapped_unmapped.fq" % (strain)
repOut = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Mito/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Mito/test_sc.tfa"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
outBWA = "alnMitotest_sc_%s_1" % strain
opt = "-n 3"
ficSam = traitementBWA.lanceBWA(outBWA,reads1,reads2,repOut,ref,opt)
ficSamInRef = deconvolueSam(ficSam)
lancePipeSamtools(ficSamInRef,ref)
ficVarFilter = lanceSamtools(ficSam,ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def varFilConc(ficPileup):
samtools = "/Volumes/BioSan/opt/samtools-0.1.8/samtools"
samtools2 = "/Volumes/BioSan/opt/samtools/samtools"
bcftools = "/Volumes/BioSan/opt/samtools/bcftools"
samtoolsPl = "/Volumes/BioSan/opt/samtools-0.1.8/misc/samtools.pl"
vcfutilsPl = "/Volumes/BioSan/opt/samtools/vcfutils.pl"
#ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Mito/test_sc.tfa"
ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Mito/Contigs4_align63-75.tfa"
# varfilter
out1 = "%s.varfilter" % ficPileup
cmd1 = "%s varFilter -d 12 -D 200000 %s &> %s" % (samtoolsPl,ficPileup,out1)
# varfilter -p
out2 = "%s-p.varfilter" % ficPileup
cmd2 = "%s varFilter -p -d 12 -D 200000 %s &> %s" % (samtoolsPl,ficPileup,out2)
os.system(cmd1)
os.system(cmd2)
traitementSamtools.fromVarfilter2tsvLike(out1)
#extrait consensus
ficBam = ficPileup.replace(".pileup","")
out3 = "%s-cns.fq" % ficPileup
cmd3 = "%s mpileup -6 -C50 -A -uf %s %s|%s view -cg -|%s vcf2fq> %s" % (samtools2,ref,ficBam,bcftools,vcfutilsPl,out3)
os.system(cmd3)
fromFq2Tfa(out3)
def lanceGenerationTsv():
liStrains = ['55-86_1','62-196','62-1041','67-588','CBS2861','CBS4104','CBS4568','CBS5828','CBS6545','CBS6547','CBS6626','CBS10367','CBS10368','dd281a','DBVPG3108','DBVPG4002','68917-2','CBS10369','CBS6546','DBVPG3452','NRBC101999','NRBC10572','NRBC10955','NRBC1811','NRBC1892']
rep = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Nuclear/MatePair"
for strain in liStrains:
print "traite %s" % strain
repStrain = "%s/%s" % (rep,strain)
ficVar = "%s/alnFin-%sPE-rel.sorted.inRef.bam.pileup.varfilter" % (repStrain,strain)
traitementSamtools.fromVarfilter2tsvLike(ficVar)
def lanceFinTraitement(strain):
ficSam1 = "%s/aln_%sSE.sam" % (strain, strain)
ficSam = "%s/aln_%sSE-rel.sorted.sam" % (strain, strain)
if not os.path.isfile(ficSam1):
ficSam = "%s/aln_%s_1PE-rel.sorted.sam" % (strain, strain)
print ficSam
ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Index/BWA/saklRef.fasta"
ficVarFilter = traitementSamtools.lanceFinPipeSamtools(ficSam, ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def demiPipe():
# liStrains = ['55-86_1','62-196','62-1041','67-588','77-1003','CBS2861','CBS4104','CBS4568','CBS5828','CBS6545','CBS6547','CBS6626','CBS10367','CBS10368','dd281a','DBVPG3108','DBVPG4002','NCYC543']
liStrains = ['62-196', '62-1041', '67-588', '77-1003', 'CBS2861', 'CBS4104', 'CBS4568', 'CBS5828', 'CBS6545',
'CBS6547', 'CBS6626', 'CBS10367', 'CBS10368', 'dd281a', 'DBVPG3108', 'DBVPG4002', 'NCYC543']
ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Index/BWA/saklRef.fasta"
rep = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Nuclear/CleanPE"
for strain in liStrains:
repStrain = "%s/%s" % (rep, strain)
ficBam = "%s/aln_%s_PE-rel.sorted.bam" % (repStrain, strain)
ficVarFilter = lanceDemiPipeSamtools(ficBam, ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeSakl(strain):
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run3/CleanPE/s_1_%s-trim.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run3/CleanPE/s_2_%s-trim.fq" % (strain)
repOut = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Nuclear/CleanPE/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Index/BWA/saklRef.fasta"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
outBWA = "aln_%s_1Bis" % strain
opt = ""
if not "Run3" in reads1:
opt += "-I"
ficSam = traitementBWA.lanceBWA(outBWA, reads1, reads2, repOut, ref, opt)
#ficSam = "%s/%sPE.sam" % (repOut,outBWA)
# conversion du ficSam traditionnel en ficSam avec Flags textuels
ficSamX = traitementSamtools.convertFlag(ficSam)
#ficSamX = "%s-X" % ficSam
# extraction des ali de reads paires de ficSam a partir des infos de ficSamX
ficSamCorrect = traitementBWA.extraitCorrectlyPairedFromSam(ficSamX, ficSam)
#ficSamCorrect = "%s/aln_%s_1BisPE.sam-correct" % (repOut,strain)
lUnmappedReads = traitementBWA.extraitUnmappedReadsPair(ficSamCorrect, reads1, reads2)
opt += " -n 8 -o 2"
outBWA2 = "aln_%s_unmapped" % strain
ficSamUnmapped = traitementBWA.lanceBWA(outBWA2, lUnmappedReads[0], lUnmappedReads[1], repOut, ref, opt)
#ficSamUnmapped = "%s/aln_%s_unmappedPE.sam" % (repOut,strain)
ficSamUnmappedInRef = traitementSamtools.deconvolueSam(ficSamUnmapped)
# concatenation des 2 fichiers sam : d abord les unmapped pour avoir le header, puis ficSamCorrected
ficSamAll = "%s/aln_%s_PE.sam" % (repOut, strain)
cmdB = "cat %s %s > %s" % (ficSamUnmappedInRef, ficSamCorrect, ficSamAll)
# a partir de celui-ci extraction des ali des paires OK
os.system(cmdB)
# je peux creer les fic de reads unmapped pour mito a partir de la aussi
# ils s appelleront xxx_unmapped_unmapped.fq
lReadsUnmappedPourMito = traitementBWA.extraitUnmappedReadsPair(ficSamUnmappedInRef, lUnmappedReads[0],
lUnmappedReads[1])
#traitementSamtools.lancePipeSamtools(ficSamAll,ref)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
ficVarFilter = traitementSamtools.lancePipeSamtools(ficSamAll, ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeIncomp16(strain,out):
reads = "/Volumes/BioSan/Users/friedrich/Incompatibilite/Reads/%s/NG-5435_%s_sequence.fastq" % (strain,strain[:-2])
repOut = "/Volumes/BioSan/Users/friedrich/Incompatibilite/BWA/Chrom16/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/Incompatibilite/ReferenceSequence/FY/Index/BWA/chrom16_350000-420000.fasta"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
ficSam = traitementBWA.lanceBWAsamse(strain,out,reads,repOut,ref)
ficSam = "%s/%sSE.sam" % (repOut,out)
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
ficVarFilter = traitementSamtools.lancePipeSamtools(ficSamInRef,ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeIncompPE(strain):
reads1 = "/Volumes/BioSan/Users/friedrich/Reads/BGI/Run1Feb2013/%s/%s_1.fq" % (strain,strain)
reads2 = "/Volumes/BioSan/Users/friedrich/Reads/BGI/Run1Feb2013/%s/%s_2.fq" % (strain,strain)
repOut = "/Volumes/BioSan/Users/jhou/Documents/Incompatibility/BWA/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/ReferenceSequence/LaKl/CBS3082/saklRef.fasta"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
opt = "-n 5 -o 1"
opt = ""
out = "aln-ref%s" % strain
ficSam = traitementBWA.lanceBWA(out,reads1,reads2,repOut,ref,opt)
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
ficVarFilter = lancePipeSamtoolsJing(ficSamInRef,ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeIncompPE(strain):
reads1 = "/Volumes/BioSan/Users/jhou/Documents/Reads/Pool-gly-R/%s_Cleandata_1.fq" % strain
reads2 = "/Volumes/BioSan/Users/jhou/Documents/Reads/Pool-gly-R/%s_Cleandata_2.fq" % strain
repOut = "/Volumes/BioSan/Users/jhou/Documents/Incompatibility/BWA/test/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/Incompatibilite/ReferenceSequence/FY/Index/BWA/FYref.tfa"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
opt = "-n 5 -o 1"
opt = ""
out = "aln-%s" % strain
ficSam = traitementBWA.lanceBWA(out,reads1,reads2,repOut,ref,opt)
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
ficVarFilter = lancePipeSamtoolsJing(ficSamInRef,ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeCramORI():
reads1 = "/Volumes/BioSan/Users/friedrich/Dikaryome/Reads/Cram/CleanPE/AQF_AFOSU_4_all_707WBAAXX-trim.fq"
#reads2 = "/Volumes/BioSan/Users/friedrich/Dikaryome/Reads/Cram/CleanPE/AQF_AFOSU_4_2_707WBAAXX-trim.fq"
repOut = "/Volumes/BioSan/Users/friedrich/Dikaryome/BWA/CramVsDeha"
ref = "/Volumes/BioSan/Users/friedrich/Dikaryome/ReferenceSequences/Deha/Index/BWA/genomeDeha.tfa"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
outBWA = "aln_CramVsDeha"
opt = "-n 8 -o 2"
ficSam = traitementBWA.lanceBWAsamse(outBWA,reads1,repOut,ref,opt)
#ficSam = "aln_CramVsDeha_1SE.sam"
# determination des unmapped reads
#lUnmappedReads = traitementBWA.extraitUnmappedReadsPair(ficSamCorrect,reads1,reads2)
# mapping de ces "unmapped" avec des parametres moins stringents
#outBWA2 = "aln_CramVsDeha_unmapped"
#ficSamUnmapped = traitementBWA.lanceBWA(outBWA2,lUnmappedReads[0],lUnmappedReads[1],repOut,ref,opt)
#ficSamUnmappedInRef = traitementSamtools.deconvolueSam(ficSamUnmapped)
# concatenation des 2 fichiers sam : d abord les unmapped pour avoir le header, puis ficSamCorrected
#ficSamAll = "%s/aln_CramVsDeha_PE.sam" % (repOut)
#cmdB = "cat %s %s > %s" % (ficSamUnmappedInRef,ficSamCorrect,ficSamAll)
# a partir de celui-ci extraction des ali des paires OK
#os.system(cmdB)
# je peux creer les fic de reads unmapped pour mito a partir de la aussi
# ils s appelleront xxx_unmapped_unmapped.fq
#lReadsUnmappedPourMito = traitementBWA.extraitUnmappedReadsPair(ficSamUnmappedInRef,lUnmappedReads[0],lUnmappedReads[1])
ficVarFilter = traitementSamtools.lancePipeSamtoolsSansRel(ficSam,ref)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeIncompSE(strain):
reads = "/Volumes/BioSan/Users/friedrich/Incompatibilite/Reads/Run5/s_%s_all-trim.fq" % (strain)
repOut = "/Volumes/BioSan/Users/friedrich/Incompatibilite/BWA/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/Incompatibilite/ReferenceSequence/FY/test_ref/FYref.fasta"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
opt = "-n 5 -o 1"
opt = ""
out = "aln-%s" % strain
ficSam = traitementBWA.lanceBWAsamse(out,reads,repOut,ref,opt)
#ficSam = "%s/%sSE.sam" % (repOut,out)
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
#ficSamInRef = "%s/%sSE.sam.inRef" % (repOut,out)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
ficVarFilter = lancePipeSamtoolsJing(ficSamInRef,ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeIncompPE(strain):
reads1 = "/Volumes/BioSan/Users/friedrich/Reads/Genoscope/1002YeastGenomes/201307/BCM_%sOSW_6_1_C2420ACXX.%s_clean.fastq" % (
strain.split("-")[0], strain.split("-")[1])
reads2 = "/Volumes/BioSan/Users/friedrich/Reads/Genoscope/1002YeastGenomes/201307/BCM_%sOSW_6_2_C2420ACXX.%s_clean.fastq" % (
strain.split("-")[0], strain.split("-")[1])
repOut = "/Volumes/BioSan/Users/friedrich/1002YeastGenomes/BWA/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/Incompatibilite/ReferenceSequence/FY/test_ref/FYref.tfa"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
opt = "-n 5 -o 1"
opt = ""
out = "aln-%s" % strain
ficSam = traitementBWA.lanceBWA(out, reads1, reads2, repOut, ref, opt)
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
ficVarFilter = lancePipeSamtoolsJing(ficSamInRef, ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeSace(strain):
reads1 = "/Volumes/BioSan/Users/ssiguenza/Projets/MiSeqDunham/RunOct2012/%s/CleanPE/s_1_%s-trim-clean.fq" % (strain,strain)
reads2 = "/Volumes/BioSan/Users/ssiguenza/Projets/MiSeqDunham/RunOct2012/%s/CleanPE/s_2_%s-trim-clean.fq" % (strain,strain)
repOut = "/Volumes/BioSan/Users/friedrich/NIH/RunOct2012/%s/n9o2" % strain
ref = "/Volumes/BioSan/Users/friedrich/Incompatibilite/ReferenceSequence/FY/Index/BWA/FYref.tfa"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
outBWA = "aln_%s" % strain
opt = "-n 9 -o 2"
#opt += " -I"
ficSamAll = traitementBWA.lanceBWA(outBWA,reads1,reads2,repOut,ref,opt)
ficSamAll = "%s/aln_%sPE.sam" % (repOut,strain)
ficVarFilter = traitementSamtools.lancePipeSamtools(ficSamAll,ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeSaklEnd(strain):
repOut = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/Nuclear/RawPE/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Index/BWA/saklRef.fasta"
lUnmappedReads = list()
lUnmappedReads.append("/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run3/s_1_%s_unmapped.fq" % strain)
lUnmappedReads.append("/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run3/s_2_%s_unmapped.fq" % strain)
ficSamCorrect = "%s/aln_%s_1BisPEBis.sam-correct" % (repOut,strain)
ficSamUnmappedInRef = "%s/aln_%s_unmappedPEBis.sam.inRef" % (repOut,strain)
ficSamAll = "%s/aln_%s_PEBis.sam" % (repOut,strain)
cmdB = "cat %s %s > %s" % (ficSamUnmappedInRef,ficSamCorrect,ficSamAll)
# a partir de celui-ci extraction des ali des paires OK
os.system(cmdB)
# je peux creer les fic de reads unmapped pour mito a partir de la aussi
# ils s appelleront xxx_unmapped_unmapped.fq
lReadsUnmappedPourMito = traitementBWA.extraitUnmappedReadsPair(ficSamUnmappedInRef,lUnmappedReads[0],lUnmappedReads[1])
#traitementSamtools.lancePipeSamtools(ficSamAll,ref)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
ficVarFilter = traitementSamtools.lancePipeSamtools(ficSamAll,ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeGono(strain):
reads1 = "/Volumes/BioSan/Users/friedrich/Reads/BGI/Run2Jan2013/%s/CleanPE/%s_Cleandata_1-trim.fq" % (
strain, strain)
reads2 = "/Volumes/BioSan/Users/friedrich/Reads/BGI/Run2Jan2013/%s/CleanPE/%s_Cleandata_2-trim.fq" % (
strain, strain)
repOut = "/Volumes/BioSan/Users/friedrich/Gonorrhoeae/BWA/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/ReferenceSequence/Gonorrhoeae/NCCP11945/NCCP11945.fasta"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
outBWA = "aln_%s" % strain
opt = ""
#opt = "-n 9 -o 2"
#opt += " -I"
#ficSamAll = traitementBWA.lanceBWA(outBWA,reads1,reads2,repOut,ref,opt)
ficSamAll = "%s/aln_%sPE.sam" % (repOut, strain)
ficVarFilter = lancePipeSamtools(ficSamAll, ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def pipeIncompMito(strain):
#reads = "/Volumes/BioSan/Users/friedrich/Incompatibilite/Reads/Run5/s_%s-trim.fq" % (strain)
#repOut = "/Volumes/BioSan/Users/friedrich/Incompatibilite/BWA/%s" % strain
ref = "/Volumes/BioSan/Users/friedrich/Incompatibilite/ReferenceSequence/FY/Index/BWA/mitoRefnew.fasta"
reads1 = "/Volumes/BioSan/Users/friedrich/Incompatibilite/Reads/Run2BGI/%s.L500_1.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/Incompatibilite/Reads/Run2BGI/%s.L500_2.fq" % (strain)
repOut = "/Volumes/BioSan/Users/jhou/Documents/Incompatibility/BWA/%s_mitoBIS" % strain
#ref = "/Volumes/BioSan/Users/friedrich/Incompatibilite/ReferenceSequence/FY/test_ref/mitoRef.fasta"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
opt = "-n 5 -o 2"
opt = ""
out = "aln-Mito%s" % strain
ficSam = traitementBWA.lanceBWA(out,reads1,reads2,repOut,ref,opt)
#ficSam = "%s/%sSE.sam" % (repOut,out)
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
ficVarFilter = lancePipeSamtoolsJing(ficSamInRef,ref)
traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)
def lanceSamtoolsSurDenovo(ficSam, ref):
# transfo du .sam en .bam
ficBam = ficSam.replace("sam", "bam")
cmd1 = "%s view -bT %s %s > %s" % (csys.SAMTOOLS, ref, ficSam, ficBam)
# trie du fichier bam
out3 = ficBam.replace("bam", "sorted")
cmd3 = "%s sort %s %s" % (csys.SAMTOOLS, ficBam, out3)
# indexation du fichier bam trie
out4 = "%s.bam" % (out3)
cmd4 = "%s index %s" % (csys.SAMTOOLS, out4)
# stats sur les alignements
out5 = "%s.readstat" % (out4)
cmd5 = "%s flagstat %s > %s" % (csys.SAMTOOLS, out4, out5)
# stats sur le recouvrement par chrom
out6 = "%s.chromstat" % (out4)
cmd6 = "%s idxstats %s > %s" % (csys.SAMTOOLS, out4, out6)
# pileup
out7 = "%s.pileupI" % out4
cmd7 = "%s pileup -c -f %s %s > %s" % (csys.SAMTOOLS, ref, out4, out7)
out7B = "%s.pileup" % out4
# varfilter
out8 = "%s.varfilter" % out7
cmd8 = "%s varFilter -q 25 -d 1 -D 200000 -N 10 %s &> %s" % (csys.SAMTOOLSPl, out7B, out8)
# varfilter -p
out9 = "%s-p.varfilter" % out7B
cmd9 = "%s varFilter -p -q 25 -d 1 -D 200000 -N 10 %s &> %s" % (csys.SAMTOOLSPl, out7B, out9)
os.system(cmd1)
os.system(cmd3)
os.system(cmd4)
os.system(cmd5)
os.system(cmd6)
os.system(cmd7)
traitementSamtools.cleanPileup(out7, out7B)
os.system(cmd8)
traitementSamtools.fromVarfilter2tsvLike(out8)
def lancePipeSamtools():
ref = "/Volumes/BioSan/Users/friedrich/ArbreJing/SequenceReference/BUSeq/s288c-R61.fasta"
allfile = glob.glob("/Volumes/BioSan/Users/friedrich/ArbreJing/BWA/*/*.sam")
allfile = glob.glob("/Volumes/BioSan/Users/friedrich/ArbreJing/BWA/CECT10266_1b/*.sam.inRef")
for ficSam in allfile:
# transfo du .sam en .bam
ficBam = ficSam.replace("sam","bam")
cmd1 = "%s view -bT %s %s > %s" % (csys.SAMTOOLS,ref,ficSam,ficBam)
# trie du fichier bam
out3 = ficBam.replace("bam","sorted")
cmd3 = "%s sort %s %s" % (csys.SAMTOOLS,ficBam,out3)
# indexation du fichier bam trie
out4 = "%s.bam" % (out3)
cmd4 = "%s index %s" % (csys.SAMTOOLS,out4)
# stats sur les alignements
out5 = "%s.readstat" % (out4)
cmd5 = "%s flagstat %s > %s" % (csys.SAMTOOLS,out4, out5)
# stats sur le recouvrement par chrom
out6 = "%s.chromstat" % (out4)
cmd6 = "%s idxstats %s > %s" % (csys.SAMTOOLS,out4, out6)
out7 = "%s.pileupI" % out4
cmd7 = "%s pileup -c -f %s %s > %s" % (csys.SAMTOOLS,ref,out4,out7)
#os.system(cmd1)
#os.system(cmd3)
#os.system(cmd4)
#os.system(cmd5)
#os.system(cmd6)
#os.system(cmd7)
out7 = "alnFin-CECT10266_1bPE-rel.sorted.inRef.bam.pileupI"
out8 = "%s.varfilter" % out7
cmd8 = "%s varFilter -d 1 %s &> %s" % (csys.SAMTOOLSPl,out7,out8)
os.system(cmd8)
traitementSamtools.fromVarfilter2tsvLike(out8)
def lanceVF2tsv(ficVarFilter): traitementSamtools.fromVarfilter2tsvLike(ficVarFilter)