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Source code for galaxy.tools.util.galaxyops

"""Utility functions for galaxyops"""

import sys

from galaxy.util import unicodify


def warn(msg):
    # TODO: since everything printed to stderr results in job.state = error, we
    # don't need both a warn and a fail...
    print(msg, file=sys.stderr)
    sys.exit(1)


def fail(msg):
    print(msg, file=sys.stderr)
    sys.exit(1)


# Default chrom, start, end, strand cols for a bed file
BED_DEFAULT_COLS = 0, 1, 2, 5


def parse_cols_arg(cols):
    """Parse a columns command line argument into a four-tuple"""
    if cols:
        # Handle case where no strand column included - in this case, cols
        # looks something like 1,2,3,
        if cols.endswith(','):
            cols += '0'
        col_list = [int(x) - 1 for x in cols.split(",")]
        return col_list
    else:
        return BED_DEFAULT_COLS


def default_printer(stream, exc, obj):
    print("%d: %s" % (obj.linenum, obj.current_line), file=stream)
    print("\tError: %s" % unicodify(exc), file=stream)


def skipped(reader, filedesc=""):
    first_line, line_contents, problem = reader.skipped_lines[0]
    return 'Skipped %d invalid lines%s, 1st line #%d: "%s", problem: %s' % (reader.skipped, filedesc, first_line, line_contents, problem)