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 extraitUnmappedCleanSE(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)
ficSamInRef = "%s/aln_%sPE.sam.inRef" % (repOut, strain)
ficSamNotInRef = ficSamInRef.replace("inRef", "notInRef")
ficSamX = traitementSamtools.convertFlag(ficSamNotInRef)
traitementBWA.extraitPEUnmappedReads(ficSamX, reads1, reads2)
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 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 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)