def spa(args):
"""
%prog spa spafiles
Convert chromosome ordering from SPA to simple lists. First column is the
reference order.
"""
from jcvi.algorithms.graph import merge_paths
from jcvi.utils.cbook import uniqify
p = OptionParser(spa.__doc__)
p.add_option(
"--unmapped",
default=False,
action="store_true",
help="Include unmapped scaffolds in the list [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
spafiles = args
paths = []
mappings = []
missings = []
for spafile in spafiles:
fp = open(spafile)
path = []
mapping = []
missing = []
for row in fp:
if row[0] == '#' or not row.strip():
continue
atoms = row.rstrip().split('\t')
if len(atoms) == 2:
a, c2 = atoms
assert a == "unmapped"
missing.append(c2)
continue
c1, c2, orientation = atoms
path.append(c1)
mapping.append(c2)
paths.append(uniqify(path))
mappings.append(mapping)
missings.append(missing)
ref = merge_paths(paths)
print "ref", len(ref), ",".join(ref)
for spafile, mapping, missing in zip(spafiles, mappings, missings):
mapping = [x for x in mapping if "random" not in x]
mapping = uniqify(mapping)
if len(mapping) < 50 and opts.unmapped:
mapping = uniqify(mapping + missing)
print spafile, len(mapping), ",".join(mapping)
def spa(args):
"""
%prog spa spafiles
Convert chromosome ordering from SPA to simple lists. First column is the
reference order.
"""
from jcvi.algorithms.graph import merge_paths
from jcvi.utils.cbook import uniqify
p = OptionParser(spa.__doc__)
p.add_option("--unmapped", default=False, action="store_true",
help="Include unmapped scaffolds in the list [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
spafiles = args
paths = []
mappings = []
missings = []
for spafile in spafiles:
fp = open(spafile)
path = []
mapping = []
missing = []
for row in fp:
if row[0] == '#' or not row.strip():
continue
atoms = row.rstrip().split('\t')
if len(atoms) == 2:
a, c2 = atoms
assert a == "unmapped"
missing.append(c2)
continue
c1, c2, orientation = atoms
path.append(c1)
mapping.append(c2)
paths.append(uniqify(path))
mappings.append(mapping)
missings.append(missing)
ref = merge_paths(paths)
print "ref", len(ref), ",".join(ref)
for spafile, mapping, missing in zip(spafiles, mappings, missings):
mapping = [x for x in mapping if "random" not in x]
mapping = uniqify(mapping)
if len(mapping) < 50 and opts.unmapped:
mapping = uniqify(mapping + missing)
print spafile, len(mapping), ",".join(mapping)
