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 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 mappingSaklCleanSE(strain):
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanPE/s_1_%s-trim.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanPE/s_2_%s-trim.fq" % (strain)
if not os.path.isfile(reads1):
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/NuclearMito/%s" % (strain)
ref = "/Volumes/BioSan/Users/friedrich/GB-3G/SequenceReference/Sakl/Index/BWA/saklRefNuclMito.fasta"
if not os.path.isdir(repOut):
os.mkdir(repOut)
cmdA = "chmod 777 %s" % repOut
os.system(cmdA)
outBWA = "aln_%s" % strain
opt = "-n 8 -o 2 "
if not "Run3" in reads1:
opt += "-I "
# print reads
ficSam = traitementBWA.lanceBWA(outBWA, reads1, reads2, repOut, ref, opt)
# conversion du ficSam traditionnel en ficSam avec Flags textuels
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
ficSamNotInRef = ficSamInRef.replace("inRef", "notInRef")
ficSamX = traitementSamtools.convertFlag(ficSamNotInRef)
traitementBWA.extraitPEUnmappedReads(ficSamX, reads1, reads2)
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 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 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 pipeSaklPE(strain, p1, p2):
reads1 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run6/CleanPE/s_1_%s-trim.fq" % (strain)
reads2 = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run6/CleanPE/s_2_%s-trim.fq" % (strain)
repOut = "/Volumes/BioSan/Users/pjung/Documents/GB-3G/BWA/Nuclear/Recombinaison/%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_1" % strain
opt = ""
if not "Run3" in reads1 and not "Run4" in reads1:
opt += "-I"
opt += " -n 8 -o 2"
ficSam = traitementBWA.lanceBWA(outBWA, reads1, reads2, repOut, ref, opt)
ficVarFilter = traitementSamtools.lancePipeSamtoolsRecomb(ficSam, ref)
ficOri = definiProvenanceSeg(strain, p1, p2)
ficOriNew = postTraiteProvenanceSeg(ficOri, strain)
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)