def tabix_index(in_file, config, preset="vcf"):
"""Index a file using tabix.
"""
in_file = os.path.abspath(in_file)
out_file = in_file + ".tbi"
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_file:
tabix = tools.get_tabix_cmd(config)
tx_in_file = os.path.splitext(tx_out_file)[0]
os.symlink(in_file, tx_in_file)
cmd = "{tabix} -p {preset} {tx_in_file}"
do.run(cmd.format(**locals()), "tabix index %s" % os.path.basename(in_file))
return out_file
def tabix_index(in_file, config, preset=None):
"""Index a file using tabix.
"""
preset = _guess_preset(in_file) if preset is None else preset
in_file = os.path.abspath(in_file)
out_file = in_file + ".tbi"
if not utils.file_exists(out_file) or not utils.file_uptodate(out_file, in_file):
with file_transaction(config, out_file) as tx_out_file:
tabix = tools.get_tabix_cmd(config)
tx_in_file = os.path.splitext(tx_out_file)[0]
utils.symlink_plus(in_file, tx_in_file)
cmd = "{tabix} -f -p {preset} {tx_in_file}"
do.run(cmd.format(**locals()), "tabix index %s" % os.path.basename(in_file))
return out_file
def tabix_index(in_file, config, preset=None):
"""Index a file using tabix.
"""
preset = _guess_preset(in_file) if preset is None else preset
in_file = os.path.abspath(in_file)
out_file = in_file + ".tbi"
if not utils.file_exists(out_file) or not utils.file_uptodate(out_file, in_file):
with file_transaction(config, out_file) as tx_out_file:
tabix = tools.get_tabix_cmd(config)
tx_in_file = os.path.splitext(tx_out_file)[0]
utils.symlink_plus(in_file, tx_in_file)
cmd = "{tabix} -f -p {preset} {tx_in_file}"
do.run(cmd.format(**locals()), "tabix index %s" % os.path.basename(in_file))
return out_file
def tabix_index(in_file, config, preset=None, tabix_args=None):
"""Index a file using tabix.
"""
in_file = os.path.abspath(in_file)
out_file = in_file + ".tbi"
if not utils.file_exists(out_file) or not utils.file_uptodate(out_file, in_file):
# Remove old index files to prevent linking into tx directory
utils.remove_safe(out_file)
with file_transaction(config, out_file) as tx_out_file:
tabix = tools.get_tabix_cmd(config)
tx_in_file = os.path.splitext(tx_out_file)[0]
utils.symlink_plus(in_file, tx_in_file)
if tabix_args:
cmd = "{tabix} -f {tabix_args} {tx_in_file}"
else:
preset = _guess_preset(in_file) if preset is None else preset
cmd = "{tabix} -f -p {preset} {tx_in_file}"
do.run(cmd.format(**locals()), "tabix index %s" % os.path.basename(in_file))
return out_file
def tabix_index(in_file, config, preset=None, tabix_args=None):
"""Index a file using tabix.
"""
in_file = os.path.abspath(in_file)
out_file = in_file + ".tbi"
if not utils.file_exists(out_file) or not utils.file_uptodate(out_file, in_file):
# Remove old index files to prevent linking into tx directory
utils.remove_safe(out_file)
with file_transaction(config, out_file) as tx_out_file:
tabix = tools.get_tabix_cmd(config)
tx_in_file = os.path.splitext(tx_out_file)[0]
utils.symlink_plus(in_file, tx_in_file)
if tabix_args:
cmd = "{tabix} -f {tabix_args} {tx_in_file}"
else:
preset = _guess_preset(in_file) if preset is None else preset
cmd = "{tabix} -f -p {preset} {tx_in_file}"
do.run(cmd.format(**locals()), "tabix index %s" % os.path.basename(in_file))
return out_file
