def _data_liftover(lift_over_genomes):
"""Download chain files for running liftOver.
Does not install liftOver binaries automatically.
"""
lo_dir = os.path.join(env.data_files, "liftOver")
if not env.safe_exists(lo_dir):
env.safe_run("mkdir %s" % lo_dir)
lo_base_url = "ftp://hgdownload.cse.ucsc.edu/goldenPath/%s/liftOver/%s"
lo_base_file = "%sTo%s.over.chain.gz"
for g1 in lift_over_genomes:
for g2 in [g for g in lift_over_genomes if g != g1]:
g2u = g2[0].upper() + g2[1:]
cur_file = lo_base_file % (g1, g2u)
non_zip = os.path.splitext(cur_file)[0]
worked = False
with cd(lo_dir):
if not env.safe_exists(non_zip):
result = shared._remote_fetch(env, "%s" % (lo_base_url % (g1, cur_file)), allow_fail=True)
# Lift over back and forths don't always exist
# Only move forward if we found the file
if result:
worked = True
env.safe_run("gunzip %s" % result)
if worked:
ref_parts = [g1, g2, os.path.join(lo_dir, non_zip)]
galaxy.update_loc_file("liftOver.loc", ref_parts)
def _data_liftover(lift_over_genomes):
"""Download chain files for running liftOver.
Does not install liftOver binaries automatically.
"""
lo_dir = os.path.join(env.data_files, "liftOver")
if not env.safe_exists(lo_dir):
env.safe_run("mkdir %s" % lo_dir)
lo_base_url = "ftp://hgdownload.cse.ucsc.edu/goldenPath/%s/liftOver/%s"
lo_base_file = "%sTo%s.over.chain.gz"
for g1 in lift_over_genomes:
for g2 in [g for g in lift_over_genomes if g != g1]:
g2u = g2[0].upper() + g2[1:]
cur_file = lo_base_file % (g1, g2u)
non_zip = os.path.splitext(cur_file)[0]
worked = False
with cd(lo_dir):
if not env.safe_exists(non_zip):
result = shared._remote_fetch(env,
"%s" % (lo_base_url %
(g1, cur_file)),
allow_fail=True)
# Lift over back and forths don't always exist
# Only move forward if we found the file
if result:
worked = True
env.safe_run("gunzip %s" % result)
if worked:
ref_parts = [g1, g2, os.path.join(lo_dir, non_zip)]
galaxy.update_loc_file("liftOver.loc", ref_parts)
