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#!/usr/bin/python3
"""
Tool for filtering a tabular data file. Fields are separated by tabs, the
header line is denoted by a '#' in the first byte, comments are denoted by
a '#' at the start of any subsequent line.
Expressions can use column names as well as numbers. The -c options allows
cutting, again using field name or numbers.
usage: %prog expression < table
-H, --header: keep header in output
-C, --comments: keep comments in output
--force-header: assume the first line is a header even if it does not start with "#"
-c, --cols=1,2: names or indexes of columns to keep
"""
import sys
import bx.tabular.io
from bx.cookbook import doc_optparse
def __main__():
# Parse command line arguments
options, args = doc_optparse.parse(__doc__)
try:
keep_header = bool(options.header)
keep_comments = bool(options.comments)
cols = []
if options.cols:
for c in options.cols.split(","):
try:
v = int(c)
except ValueError:
v = c
cols.append(v)
if len(args) > 0:
expr = args[0]
else:
expr = None
if options.force_header:
force_header = bx.tabular.io.FIRST_LINE_IS_HEADER
else:
force_header = None
except Exception:
doc_optparse.exception()
# Compile expression for SPEED
if expr:
expr = compile(expr, "<expr arg>", "eval")
for element in bx.tabular.io.TableReader(sys.stdin, force_header=force_header):
if isinstance(element, bx.tabular.io.Header):
if keep_header:
if cols:
print("#" + "\t".join(element[c] for c in cols))
else:
print(element)
elif isinstance(element, bx.tabular.io.Comment):
if keep_comments:
print(element)
else:
if expr is None or bool(eval(expr, {"row": element})):
if cols:
print("\t".join(element[c] for c in cols))
else:
print(element)
if __name__ == "__main__":
__main__()
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