def pipeIncompForAssembly(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/%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 0 -o 0"
ficSam = traitementBWA.lanceBWAsamse(strain,out,reads,repOut,ref,opt)
ficSamX = traitementSamtools.convertFlag(ficSam)
lUnmappedReads = traitementBWA.extraitUnmappedReads(ficSam,reads)
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 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 pipeMDR(strain):
#reads = "/Volumes/BioSan/Users/friedrich/MDR/Reads/Run5/s_%s-trim.fq" % (strain)
#reads = "/Volumes/BioSan/Users/friedrich/MDR/Reads/Run5c/CleanSE/s_%s-trim.fq" % (strain)
reads = "/Volumes/BioSan/Users/friedrich/Incompatibilite/Reads/YJM326_1/NG-5435_YJM326_sequence.fastq-trim.fastq"
#repOut = "/Volumes/BioSan/Users/friedrich/MDR/BWA/%s" % strain
repOut = "/Volumes/BioSan/Users/friedrich/Incompatibilite/Reads/YJM326_1"
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 = "-n 0 -o 0"
out = "alnFin-%s" % strain
ficSam = traitementBWA.lanceBWAsamse(out, reads, repOut, ref, opt)
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
# 1ere etape est de retirer les ali avec flag ? a 0 dans les bam
ficVarFilter = traitementSamtools.lancePipeSamtools(ficSamInRef, ref)
fromVarfilter2tsvLikeCyrielle(ficVarFilter)
def pipeSaklSE(strain, p1, p2):
reads = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/Run5/s_%s_all-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" % strain
opt = ""
if not "Run3" in reads and not "Run4" in reads and not "Run5" in reads:
opt += "-I"
opt += " -n 5 -o 1"
ficSam = traitementBWA.lanceBWAsamse(outBWA, reads, repOut, ref, opt)
ficVarFilter = traitementSamtools.lancePipeSamtoolsRecomb(ficSam, ref)
ficOri = definiProvenanceSeg(strain, p1, p2)
#ficOri = "ori81b.tab"
ficOriNew = postTraiteProvenanceSeg(ficOri, strain)
def mappingSaklCleanSEOld(strain):
reads = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanSE30strains/s_%s-trim.fq" % (strain)
if not os.path.isfile(reads):
reads = "/Volumes/BioSan/Users/friedrich/GB-3G/Reads/CleanSE30strains/Run3/s_%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 reads:
opt += "-I "
print reads
ficSam = traitementBWA.lanceBWAsamse(outBWA, reads, repOut, ref, opt)
# ficSam = "/Volumes/BioSan/Users/friedrich/GB-3G/BWA/NuclearMito/55-86_1/aln_55-86_1SE.sam"
ficSamInRef = traitementSamtools.deconvolueSam(ficSam)
ficSamX = traitementSamtools.convertFlag(ficSamInRef)
unmappedReads = traitementBWA.extraitUnmappedReads(ficSamX, reads)
