def group(args):
"""
%prog group tabfile > tabfile.grouped
Given a tab-delimited file, either group all elements within the file or
group the elements in the value column(s) based on the key (groupby) column
For example, convert this | into this
---------------------------------------
a 2 3 4 | a,2,3,4,5,6
a 5 6 | b,7,8
b 7 8 | c,9,10,11
c 9 |
c 10 11 |
If grouping by a particular column,
convert this | into this:
---------------------------------------------
a 2 3 4 | a 2,5 3,6 4
a 5 6 | b 7 8
b 7 8 | c 9,10 11
c 9 |
c 10 11 |
By default, it uniqifies all the grouped elements
"""
from jcvi.utils.cbook import AutoVivification
from jcvi.utils.grouper import Grouper
p = OptionParser(group.__doc__)
p.set_sep()
p.add_option("--groupby",
default=None,
type="int",
help="Default column to groupby")
p.add_option("--groupsep",
default=",",
help="Separator to join the grouped elements")
p.add_option(
"--nouniq",
default=False,
action="store_true",
help="Do not uniqify the grouped elements",
)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(tabfile, ) = args
sep = opts.sep
groupby = opts.groupby
groupsep = opts.groupsep
cols = []
grouper = AutoVivification() if groupby is not None else Grouper()
fp = must_open(tabfile)
for row in fp:
row = row.rstrip()
atoms = row.split(sep)
if groupby is not None:
if len(cols) < len(atoms):
cols = [x for x in range(len(atoms))]
if groupby not in cols:
logging.error(
"groupby col index `{0}` is out of range".format(groupby))
sys.exit()
key = atoms[groupby]
for col in cols:
if col == groupby:
continue
if not grouper[key][col]:
grouper[key][col] = [] if opts.nouniq else set()
if col < len(atoms):
if groupsep in atoms[col]:
for atom in atoms[col].split(groupsep):
if opts.nouniq:
grouper[key][col].append(atom)
else:
grouper[key][col].add(atom)
else:
if opts.nouniq:
grouper[key][col].append(atoms[col])
else:
grouper[key][col].add(atoms[col])
else:
grouper.join(*atoms)
for key in grouper:
if groupby is not None:
line = []
for col in cols:
if col == groupby:
line.append(key)
elif col in grouper[key].keys():
line.append(groupsep.join(grouper[key][col]))
else:
line.append("na")
print(sep.join(line))
else:
print(groupsep.join(key))
def group(args):
"""
%prog group tabfile > tabfile.grouped
Given a tab-delimited file, either group all elements within the file or
group the elements in the value column(s) based on the key (groupby) column
For example, convert this | into this
---------------------------------------
a 2 3 4 | a,2,3,4,5,6
a 5 6 | b,7,8
b 7 8 | c,9,10,11
c 9 |
c 10 11 |
If grouping by a particular column,
convert this | into this:
---------------------------------------------
a 2 3 4 | a 2,5 3,6 4
a 5 6 | b 7 8
b 7 8 | c 9,10 11
c 9 |
c 10 11 |
By default, it uniqifies all the grouped elements
"""
from jcvi.utils.cbook import AutoVivification
from jcvi.utils.grouper import Grouper
p = OptionParser(group.__doc__)
p.set_sep()
p.add_option("--groupby", default=None, type='int',
help="Default column to groupby [default: %default]")
p.add_option("--groupsep", default=',',
help="Separator to join the grouped elements [default: `%default`]")
p.add_option("--nouniq", default=False, action="store_true",
help="Do not uniqify the grouped elements [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
tabfile, = args
sep = opts.sep
groupby = opts.groupby
groupsep = opts.groupsep
cols = []
grouper = AutoVivification() if groupby is not None else Grouper()
fp = must_open(tabfile)
for row in fp:
row = row.rstrip()
atoms = row.split(sep)
if groupby is not None:
if len(cols) < len(atoms):
cols = [x for x in xrange(len(atoms))]
if groupby not in cols:
logging.error("groupby col index `{0}` is out of range".format(groupby))
sys.exit()
key = atoms[groupby]
for col in cols:
if col == groupby:
continue
if not grouper[key][col]:
grouper[key][col] = [] if opts.nouniq else set()
if col < len(atoms):
if groupsep in atoms[col]:
for atom in atoms[col].split(groupsep):
if opts.nouniq:
grouper[key][col].append(atom)
else:
grouper[key][col].add(atom)
else:
if opts.nouniq:
grouper[key][col].append(atoms[col])
else:
grouper[key][col].add(atoms[col])
else:
grouper.join(*atoms)
for key in grouper:
if groupby is not None:
line = []
for col in cols:
if col == groupby:
line.append(key)
elif col in grouper[key].keys():
line.append(groupsep.join(grouper[key][col]))
else:
line.append("na")
print sep.join(line)
else:
print groupsep.join(key)
