def index(ref_file, out_dir, data):
"""Create a bismark index in the defined reference directory.
"""
(ref_dir, local_file) = os.path.split(ref_file)
gtf_file = dd.get_gtf_file(data)
bismark = config_utils.find_program("bismark", data["config"])
if not utils.file_exists(gtf_file):
raise ValueError("%s not found, could not create a star index." %
(gtf_file))
if not utils.file_exists(out_dir):
with tx_tmpdir(data, os.path.dirname(out_dir)) as tx_out_dir:
num_cores = dd.get_cores(data)
cmd = "{bismark} --bowtie2 -p {num_cores} -n 1 -o {tx_out_dir} --basename {sample} --unmapped {ref_file} {in_fastq}"
do.run(cmd.format(**locals()), "Index STAR")
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
shutil.move(tx_out_dir, out_dir)
return out_dir
def index(ref_file, out_dir, data):
"""Create a bismark index in the defined reference directory.
"""
(ref_dir, local_file) = os.path.split(ref_file)
gtf_file = dd.get_transcriptome_gtf(data, default=dd.get_gtf_file(data))
bismark = config_utils.find_program("bismark", data["config"])
if not utils.file_exists(gtf_file):
raise ValueError("%s not found, could not create a bismark index." % (gtf_file))
if not utils.file_exists(out_dir):
with tx_tmpdir(data, os.path.dirname(out_dir)) as tx_out_dir:
num_cores = dd.get_cores(data)
other_opts = config_utils.get_resources("bismark", data["config"]).get("options", [])
other_opts = " ".join([str(x) for x in other_opts]).strip()
cmd = "{bismark} {other_opts} --bowtie2 -p {num_cores} -n 1 -o {tx_out_dir} --basename {sample} --unmapped {ref_file} {in_fastq}"
do.run(cmd.format(**locals()), "Index STAR")
if os.path.exists(out_dir):
shutil.rmtree(out_dir)
shutil.move(tx_out_dir, out_dir)
return out_dir