Python FreebayesPipe.getsamfilelist Examples

Example #1

File: prepareSNP.py Project: chen318liang/call_snp_pipeline

def pre_DNA_fq(refseq):
    ref = FreebayesPipe()
    ref.pre_ref(refseq)
    step1 = FreebayesPipe()
    step1.getfqfilelist()
    print step1.namelist
    step1.pre_bwa(refseq)
    step1.runbwafile(refseq)

    step2 = FreebayesPipe()
    step2.getsamfilelist()
    print step2.namelist
    step2.runsam2bamfile()

    step3 = FreebayesPipe()
    step3.getbamfilelist()
    print step3.namelist
    step3.runsortfile()

    step4 = FreebayesPipe()
    step4.getsortfilelist()
    print step4.namelist
    step4.runrmdupfile()

    step5 = FreebayesPipe()
    step5.getrmpfilelist()
    print step5.namelist
    step5.runbaifile()
    print 'done~'

Example #2

File: prepareSNP.py Project: chen318liang/call_snp_pipeline

def pre_DNA_sam():
    step2 = FreebayesPipe()
    step2.getsamfilelist()
    print step2.namelist
    step2.runsam2bamfile()

    step3 = FreebayesPipe()
    step3.getbamfilelist()
    print step3.namelist
    step3.runsortfile()

    step4 = FreebayesPipe()
    step4.getsortfilelist()
    print step4.namelist
    step4.runrmdupfile()

    step5 = FreebayesPipe()
    step5.getrmpfilelist()
    print step5.namelist
    step5.runbaifile()
    print 'done~'