Python replaceReads Examples

Example #1

File: addindel.py Project: elephanthunter/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()

Example #2

File: addsnv.py Project: jpfeil/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()

Example #3

File: addsv.py Project: huyvuong/bamsurgeon

def replace(origbamfile, mutbamfile, outbamfile, excludefile):
    ''' 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)

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

Example #4

def replace(origbamfile, mutbamfile, outbamfile, excludefile, keepsecondary=False):
    ''' 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)

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

Example #5

File: addsv.py Project: jpfeil/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()

Example #6

File: addsv.py Project: nordhuang/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()