def run(datatype, columns, input):
# import modules locally
import sh
if input:
sh.mlr('--tsv',
'cut',
'-x',
'-f',
columns,
input,
_out=sys.stdout,
_err=sys.stderr)
elif not sys.stdin.isatty():
print('reading from stdin')
# print(sh.cat(_in=sys.stdin))
print(
sh.mlr('--tsv',
'cut',
'-x',
'-f',
columns,
_in=sys.stdin,
_out=sys.stdout,
_err=sys.stderr))
else:
parser.print_help()
def run(datatype, columns, input):
# import modules locally
import socket
import sh # type: ignore
from kgtk.exceptions import KGTKException
try:
if input:
print(input)
sh.mlr('--tsv',
'cut',
'-x',
'-f',
columns,
input,
_out=sys.stdout,
_err=sys.stderr)
elif not sys.stdin.isatty():
print(
sh.mlr('--tsv',
'cut',
'-x',
'-f',
columns,
_in=sys.stdin,
_out=sys.stdout,
_err=sys.stderr))
else:
raise KGTKException
except:
raise KGTKException
def run(datatype, pattern, input, subj_col, pred_col, obj_col):
# import modules locally
import socket
import sh # type: ignore
from kgtk.exceptions import KGTKException
props = [subj_col, pred_col, obj_col]
def prepare_filter(property, prop_pattern):
prop_pattern = prop_pattern.strip()
prop_filters = []
for value in prop_pattern.split(','):
value = value.strip()
value_filter = '$%s == "%s"' % (property, value)
prop_filters.append(value_filter)
return '(%s)' % ' || '.join(prop_filters)
try:
n1_filter, lbl_filter, n2_filter = pattern.split(';')
filters = []
for i, col_filter in enumerate([n1_filter, lbl_filter, n2_filter]):
if col_filter.strip():
ready = prepare_filter(props[i], col_filter)
filters.append(ready)
filter_str = '\'%s\'' % ' && '.join(filters)
if filter_str:
if input:
sh.mlr('--%s' % datatype,
'filter',
filter_str,
input,
_out=sys.stdout,
_err=sys.stderr)
elif not sys.stdin.isatty():
sh.mlr('--%s' % datatype,
'filter',
filter_str,
_in=sys.stdin,
_out=sys.stdout,
_err=sys.stderr)
except:
raise KGTKException
def run(datatype, property, value, input):
# import modules locally
import socket
import sh
filter = '$%s == "%s"' % (property, value)
if input:
sh.mlr('--%s' % datatype,
'filter',
filter,
input,
_out=sys.stdout,
_err=sys.stderr)
elif not sys.stdin.isatty():
sh.mlr('--%s' % datatype,
'filter',
filter,
_in=sys.stdin,
_out=sys.stdout,
_err=sys.stderr)
def run(datatype, column, input):
# import modules locally
import socket
import sh
sh.mlr('--%s' % datatype, 'sort', '-f', column, input, _out=sys.stdout, _err=sys.stderr)