csv_cut.py - select columns from a table

Tags

Python

Purpose

extract named columns from a csv formatted table

Todo

describe purpose of the script.

Usage

Extract the two columns gene and length from a table in standard input:

python csv_cut.py gene length < stdin

The script permits the use of patterns. For example, the command will select the column gene and all columns that contain the part ‘len’:

python csv_cut.py gene %len% < stdin

Type:

python csv_cut.py --help

for command line help.

Command line options

usage: csv-cut [-h] [-r] [-u] [-l] [-f FILENAME_FIELDS] [--timeit TIMEIT_FILE]
               [--timeit-name TIMEIT_NAME] [--timeit-header]
               [--random-seed RANDOM_SEED] [-v LOGLEVEL]
               [--log-config-filename LOG_CONFIG_FILENAME]
               [--tracing {function}] [-? ?] [--csv-dialect CSV_DIALECT]
               [-I STDIN] [-L STDLOG] [-E STDERR] [-S STDOUT]
csv-cut: error: argument -?: expected one argument