combine_tables.py - join tables

Tags

Python

Purpose

This script reads several tab-separated tables and joins them into a single one.

Todo

• Rename to tables2table.py

• Use pandas dataframes for fast IO and merging/joining

Usage

The option --header-names sets the column titles explicitely. Add --skip-titles if you want to avoid echoing the original title in the input files.

Example:

python combine_tables.py --help

Type:

python combine_tables.py --help

for command line help.

Command line options

usage: combine-tables [-h] [--version] [-t] [--ignore-titles] [-i]
                      [-m MISSING_VALUE] [--header-names HEADERS] [-c COLUMNS]
                      [-k TAKE] [-g GLOB] [-s SORT] [-e] [-a CAT]
                      [--sort-keys {numeric,alphabetic}] [--keep-empty]
                      [--ignore-empty] [--add-file-prefix] [--use-file-prefix]
                      [--prefixes PREFIXES] [--regex-filename REGEX_FILENAME]
                      [--regex-start REGEX_START] [--regex-end REGEX_END]
                      [--test TEST] [--timeit TIMEIT_FILE]
                      [--timeit-name TIMEIT_NAME] [--timeit-header]
                      [--random-seed RANDOM_SEED] [-v LOGLEVEL]
                      [--log-config-filename LOG_CONFIG_FILENAME]
                      [--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
                      [-E STDERR] [-S STDOUT]
combine-tables: error: argument -?: expected one argument