How to use the pyranges.read_bed function in pyranges

def test_read_bed():

    pr.read_bed("pyranges/example_data/chipseq.bed")

def test_read_bed():

    pr.read_bed("pyranges/example_data/chipseq.bed")

def test_pyranges_to_intervals():
    pranges = pyranges.read_gtf(gtf_file)
    intervals = list(pyranges_to_intervals(pranges, interval_attrs=[
        'gene_id', 'gene_name', 'transcript_id', 'exon_id']))

    assert len(intervals) == 5
    assert intervals[4].attrs['gene_id'] == 'ENSG00000012048'
    assert intervals[4].attrs['gene_name'] == 'BRCA1'
    assert intervals[4].attrs['transcript_id'] == 'ENST00000357654'
    assert intervals[4].attrs['exon_id'] == 'ENSE00003510592'

    pranges = pyranges.read_bed(example_intervals_bed)
    intervals = list(pyranges_to_intervals(pranges))

    assert len(intervals) == 4
    assert intervals[0].start == 2

    assert pranges.Chromosome.tolist() == ['chr1'] * 4
    assert pranges.Start.tolist() == [2, 2, 2, 602]
    assert pranges.End.tolist() == [1000, 5000, 1002, 604]

>>> # | chr2         | 0         | 243199373 |
    >>> # | chr3         | 0         | 198022430 |
    >>> # | chr4         | 0         | 191154276 |
    >>> # | ...          | ...       | ...       |
    >>> # | chrY         | 0         | 59373566  |
    >>> # | chrX         | 0         | 155270560 |
    >>> # | chrM         | 0         | 16571     |
    >>> # | chr22        | 0         | 51304566  |
    >>> # +--------------+-----------+-----------+
    >>> # Unstranded PyRanges object has 25 rows and 3 columns from 25 chromosomes.
    >>> # For printing, the PyRanges was sorted on Chromosome.
    """

    full_path = get_example_path("chromsizes.bed")

    return pr.read_bed(full_path)

>>> # | chrX         | 135574120 | 135574598 | NM_001727_exon_2_0_chrX_135574121_f    | 0         | +            |
    >>> # | chrX         | 47868945  | 47869126  | NM_205856_exon_4_0_chrX_47868946_f     | 0         | +            |
    >>> # | chrX         | 77294333  | 77294480  | NM_000052_exon_17_0_chrX_77294334_f    | 0         | +            |
    >>> # | ...          | ...       | ...       | ...                                    | ...       | ...          |
    >>> # | chrY         | 15409586  | 15409728  | NR_047633_exon_3_0_chrY_15409587_r     | 0         | -            |
    >>> # | chrY         | 15478146  | 15478273  | NR_047634_exon_18_0_chrY_15478147_r    | 0         | -            |
    >>> # | chrY         | 15360258  | 15361762  | NR_047601_exon_0_0_chrY_15360259_r     | 0         | -            |
    >>> # | chrY         | 15467254  | 15467278  | NM_001258270_exon_13_0_chrY_15467255_r | 0         | -            |
    >>> # +--------------+-----------+-----------+----------------------------------------+-----------+--------------+
    >>> # Stranded PyRanges object has 1,000 rows and 6 columns from 2 chromosomes.
    >>> # For printing, the PyRanges was sorted on Chromosome and Strand.
    """

    full_path = get_example_path("exons.bed")

    return pr.read_bed(full_path)

>>> # | chr1         | 9953      | 10152     | H3K27me3   | 5         | +            |
    >>> # | chr1         | 10024     | 10223     | H3K27me3   | 1         | +            |
    >>> # | chr1         | 10246     | 10445     | H3K27me3   | 4         | +            |
    >>> # | ...          | ...       | ...       | ...        | ...       | ...          |
    >>> # | chr1         | 9978      | 10177     | H3K27me3   | 7         | -            |
    >>> # | chr1         | 10001     | 10200     | H3K27me3   | 5         | -            |
    >>> # | chr1         | 10127     | 10326     | H3K27me3   | 1         | -            |
    >>> # | chr1         | 10241     | 10440     | H3K27me3   | 6         | -            |
    >>> # +--------------+-----------+-----------+------------+-----------+--------------+
    >>> # Stranded PyRanges object has 11 rows and 6 columns from 1 chromosomes.
    >>> # For printing, the PyRanges was sorted on Chromosome and Strand.
    """

    full_path = get_example_path("aorta.bed")

    return pr.read_bed(full_path)

>>> # | chr1         | 169887529 | 169887554 | U0         | 0         | +            |
    >>> # | chr1         | 216711011 | 216711036 | U0         | 0         | +            |
    >>> # | chr1         | 144227079 | 144227104 | U0         | 0         | +            |
    >>> # | ...          | ...       | ...       | ...        | ...       | ...          |
    >>> # | chrY         | 15224235  | 15224260  | U0         | 0         | -            |
    >>> # | chrY         | 13517892  | 13517917  | U0         | 0         | -            |
    >>> # | chrY         | 8010951   | 8010976   | U0         | 0         | -            |
    >>> # | chrY         | 7405376   | 7405401   | U0         | 0         | -            |
    >>> # +--------------+-----------+-----------+------------+-----------+--------------+
    >>> # Stranded PyRanges object has 10,000 rows and 6 columns from 24 chromosomes.
    >>> # For printing, the PyRanges was sorted on Chromosome and Strand.
    """

    full_path = get_example_path("chipseq.bed")

    return pr.read_bed(full_path)

def _read_intervals(gtf_path=None, bed_path=None, pranges=None,
                        intervals=None, interval_attrs=None, duplicate_attr=False):
        alternatives = [bed_path, pranges, intervals, gtf_path]
        if sum(i is not None for i in alternatives) != 1:
            raise ValueError('only one of `gth_path`, `bed_path`, `pranges`,'
                             '`intervals` or should given as input.')
        if gtf_path:
            import pyranges
            pranges = pyranges.read_gtf(gtf_path, duplicate_attr=duplicate_attr)

        elif bed_path:
            import pyranges
            pranges = pyranges.read_bed(bed_path)

        elif intervals:
            if interval_attrs is not None:
                raise ValueError(
                    '`interval_attrs` is not valid with `intervals`')

            pranges = intervals_to_pyranges(intervals)
            pranges.intervals = intervals

        return pranges