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#!/usr/bin/python3
"""
Tool for adding a column to a table. Expressions for the column are similar
to those supported by table_filter.py
usage: %prog expression colname < table
-H, --header: keep header in output
-C, --comments: keep comments in output
"""
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)
expr = args[0]
colname = args[1]
except Exception:
doc_optparse.exception()
# Compile expression for SPEED
if expr:
expr = compile(expr, "<expr arg>", "eval")
for element in bx.tabular.io.Reader(sys.stdin):
if isinstance(element, bx.tabular.io.Header):
if keep_header:
print(str(element) + "\t" + colname)
elif isinstance(element, bx.tabular.io.Comment):
if keep_comments:
print(element)
else:
val = eval(expr, {"row": element})
print(str(element) + "\t" + str(val))
if __name__ == "__main__":
__main__()
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