formatToWiki

#! /usr/bin/env python3

import yaml
import sys
import os
import docopt

doc = """
formatToWiki

Creates a Wiki table using the information in library info file.

Usage:
    formatToWiki <file>

Options:
    <file>        Library info YAML file
    -h, --help    Show help
"""


def format_to_wiki(content):
    lines = []
    lines.append("{| class='sortable'")
    lines.append("|-\n!Library Name")
    lines.append("!Reference genome")
    lines.append("!Description")
    for library, value in content["libraries"].items():
        lines.append("|-")
        lines.append(f"|{library}")
        lines.append(f"|{value['genome']}")
        lines.append(f"|{value['description']}")

    lines.append("|}")

    # apparentlty "writelines" does not add line separators
    return [f"{x}\n" for x in lines]


if __name__ == "__main__":
    args = docopt.docopt(doc, version="0.1")
    if not os.path.exists(args["<file>"]):
        sys.stderr.write(f"{args['<file>']} not found. Exit\n")
        sys.exit(1)

    with open(args["<file>"]) as f:
        content = yaml.safe_load(f.read())

    sys.stdout.writelines(format_to_wiki(content))