def sam2bam(sam_fhand, bam_fhand, header=None):
'It converts between bam and sam.'
sam_fhand.seek(0)
if header is not None:
pass
cmd = ['samtools', 'view', '-bSh', '-o', bam_fhand.name, sam_fhand.name]
call(cmd, raise_on_error=True)
bam_fhand.flush()
def bam2sam(bam_fhand, sam_fhand, header=False):
'''It converts between bam and sam.'''
bam_fhand.seek(0)
cmd = ['samtools', 'view', bam_fhand.name, '-o', sam_fhand.name]
if header:
cmd.insert(2, '-h')
call(cmd, raise_on_error=True)
sam_fhand.flush()
def get_bam_header(bam_fhand, header_fhand):
'It gets the header of the bam'
cmd = ['samtools', 'view', '-H', bam_fhand.name, '-o', header_fhand.name]
call(cmd, raise_on_error=True)