comparison breakdancer.py @ 19:87a6ec1e2400 draft

Uploaded

18:d26b184866b4

tmp_dir = tempfile.mkdtemp()
errorFile = tmp_dir+"/errorLog"

currentDir = os.path.dirname(os.path.abspath(__file__))
bam2cfg_path = currentDir+"/bam2cfg.pl"
# breakdancer_path = "/usr/bin/breakdancer-max"
breakdancer_path = "breakdancer-max"
breakdancer2vcf_path = currentDir+"/breakdancer2vcf.py"


def bam2cfg(args):
	config = tmp_dir+"/breakdancer_config"
	cmd = 'perl %s %s' % (bam2cfg_path, args.input_bam)
	execute(cmd, output=config)
	print ("\ncmd = %s  \n" ) %(cmd)
	return config


def breakdancer(args, config):
	cmd = '%s %s' % (breakdancer_path, config)
	execute(cmd, output=args.output_raw)


def breakdancer2vcf(args):
	cmd = "python %s -i %s -o %s" % ( breakdancer2vcf_path, args.output_raw, args.output_vcf )
	execute(cmd)


def execute( cmd, output="" ):
	try: 

19:87a6ec1e2400

tmp_dir = tempfile.mkdtemp()
errorFile = tmp_dir+"/errorLog"

currentDir = os.path.dirname(os.path.abspath(__file__))
bam2cfg = "./bam2cfg.pl"
# breakdancer = "/usr/bin/breakdancer-max"
breakdancer = "breakdancer-max"
breakdancer2vcf = "./breakdancer2vcf.py"


def bam2cfg(args):
	config = tmp_dir+"/breakdancer_config"
	cmd = 'perl %s %s' % (bam2cfg, args.input_bam)
	execute(cmd, output=config)
	print ("\ncmd = %s  \n" ) %(cmd)
	return config


def breakdancer(args, config):
	cmd = '%s %s' % (breakdancer, config)
	execute(cmd, output=args.output_raw)


def breakdancer2vcf(args):
	cmd = "python %s -i %s -o %s" % ( breakdancer2vcf, args.output_raw, args.output_vcf )
	execute(cmd)


def execute( cmd, output="" ):
	try: