Python replaceReads 예제들

예제 #1

파일: addsnv.py 프로젝트: zpeng1989/bamsurgeon

def replace(origbamfile, mutbamfile, outbamfile, seed=None):
    ''' open .bam file and call replacereads
    '''
    origbam = pysam.Samfile(origbamfile, 'rb')
    mutbam = pysam.Samfile(mutbamfile, 'rb')
    outbam = pysam.Samfile(outbamfile, 'wb', template=origbam)

    rr.replaceReads(origbam, mutbam, outbam, keepqual=True, seed=seed)

    origbam.close()
    mutbam.close()
    outbam.close()

예제 #2

파일: addsv.py 프로젝트: MischaLundberg/bamsurgeon

def replace(origbamfile, mutbamfile, outbamfile, excludefile, keepsecondary=False, seed=None):
    ''' open .bam file and call replacereads
    '''
    origbam = pysam.Samfile(origbamfile, 'rb')
    mutbam  = pysam.Samfile(mutbamfile, 'rb')
    outbam  = pysam.Samfile(outbamfile, 'wb', template=origbam)

    rr.replaceReads(origbam, mutbam, outbam, excludefile=excludefile, allreads=True, keepsecondary=keepsecondary, seed=seed)

    origbam.close()
    mutbam.close()
    outbam.close()

예제 #3

파일: addindel.py 프로젝트: MischaLundberg/bamsurgeon

def replace(origbamfile, mutbamfile, outbamfile, seed=None):
    ''' open .bam file and call replacereads
    '''
    origbam = pysam.Samfile(origbamfile, 'rb')
    mutbam  = pysam.Samfile(mutbamfile, 'rb')
    outbam  = pysam.Samfile(outbamfile, 'wb', template=origbam)

    rr.replaceReads(origbam, mutbam, outbam, keepqual=True, seed=seed)

    origbam.close()
    mutbam.close()
    outbam.close()

예제 #4

파일: addsv.py 프로젝트: BioInfoTools/bamsurgeon

def replace(origbamfile,
            mutbamfile,
            outbamfile,
            excludefile,
            keepsecondary=False,
            seed=None):
    ''' open .bam file and call replacereads
    '''
    origbam = pysam.Samfile(origbamfile, 'rb')
    mutbam = pysam.Samfile(mutbamfile, 'rb')
    outbam = pysam.Samfile(outbamfile, 'wb', template=origbam)

    rr.replaceReads(origbam,
                    mutbam,
                    outbam,
                    excludefile=excludefile,
                    allreads=True,
                    keepsecondary=keepsecondary,
                    seed=seed)

    origbam.close()
    mutbam.close()
    outbam.close()