How to use bioframe - 10 common examples

To help you get started, we’ve selected a few bioframe examples, based on popular ways it is used in public projects.

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mirnylab / bioframe / tests / test_region.py View on Github

def test_parse_region():
    # UCSC-style names
    assert parse_region("chr21") == ("chr21", 0, None)
    assert parse_region("chr21:1000-2000") == ("chr21", 1000, 2000)
    assert parse_region("chr21:1,000-2,000") == ("chr21", 1000, 2000)

    # Ensembl style names
    assert parse_region("6") == ("6", 0, None)
    assert parse_region("6:1000-2000") == ("6", 1000, 2000)
    assert parse_region("6:1,000-2,000") == ("6", 1000, 2000)

    # FASTA style names
    assert parse_region("gb|accession|locus") == ("gb|accession|locus", 0, None,)
    assert parse_region("gb|accession|locus:1000-2000") == (
        "gb|accession|locus",
        1000,
        2000,
    )
    assert parse_region("gb|accession|locus:1,000-2,000") == (
        "gb|accession|locus",

mirnylab / bioframe / tests / test_region.py View on Github

1000,
        2000,
    )

    # Punctuation in names (aside from :)
    assert parse_region("name-with-hyphens-") == ("name-with-hyphens-", 0, None,)
    assert parse_region("GL000207.1") == ("GL000207.1", 0, None)
    assert parse_region("GL000207.1:1000-2000") == ("GL000207.1", 1000, 2000)

    # Trailing dash
    assert parse_region("chr21:1000-") == ("chr21", 1000, None)

    # Humanized units
    assert parse_region("6:1kb-2kb") == ("6", 1000, 2000)
    assert parse_region("6:1k-2000") == ("6", 1000, 2000)
    assert parse_region("6:1kb-2M") == ("6", 1000, 2000000)
    assert parse_region("6:1Gb-") == ("6", 1000000000, None)

    with pytest.raises(ValueError):
        parse_region("chr1:2,000-1,000")  # reverse selection
        parse_region("chr1::1000-2000")  # more than one colon

mirnylab / bioframe / tests / test_region.py View on Github

2000,
    )

    # Punctuation in names (aside from :)
    assert parse_region("name-with-hyphens-") == ("name-with-hyphens-", 0, None,)
    assert parse_region("GL000207.1") == ("GL000207.1", 0, None)
    assert parse_region("GL000207.1:1000-2000") == ("GL000207.1", 1000, 2000)

    # Trailing dash
    assert parse_region("chr21:1000-") == ("chr21", 1000, None)

    # Humanized units
    assert parse_region("6:1kb-2kb") == ("6", 1000, 2000)
    assert parse_region("6:1k-2000") == ("6", 1000, 2000)
    assert parse_region("6:1kb-2M") == ("6", 1000, 2000000)
    assert parse_region("6:1Gb-") == ("6", 1000000000, None)

    with pytest.raises(ValueError):
        parse_region("chr1:2,000-1,000")  # reverse selection
        parse_region("chr1::1000-2000")  # more than one colon

mirnylab / bioframe / tests / test_region.py View on Github

assert parse_region("gb|accession|locus") == ("gb|accession|locus", 0, None,)
    assert parse_region("gb|accession|locus:1000-2000") == (
        "gb|accession|locus",
        1000,
        2000,
    )
    assert parse_region("gb|accession|locus:1,000-2,000") == (
        "gb|accession|locus",
        1000,
        2000,
    )

    # Punctuation in names (aside from :)
    assert parse_region("name-with-hyphens-") == ("name-with-hyphens-", 0, None,)
    assert parse_region("GL000207.1") == ("GL000207.1", 0, None)
    assert parse_region("GL000207.1:1000-2000") == ("GL000207.1", 1000, 2000)

    # Trailing dash
    assert parse_region("chr21:1000-") == ("chr21", 1000, None)

    # Humanized units
    assert parse_region("6:1kb-2kb") == ("6", 1000, 2000)
    assert parse_region("6:1k-2000") == ("6", 1000, 2000)
    assert parse_region("6:1kb-2M") == ("6", 1000, 2000000)
    assert parse_region("6:1Gb-") == ("6", 1000000000, None)

    with pytest.raises(ValueError):
        parse_region("chr1:2,000-1,000")  # reverse selection
        parse_region("chr1::1000-2000")  # more than one colon

mirnylab / bioframe / tests / test_region.py View on Github

1000,
        2000,
    )
    assert parse_region("gb|accession|locus:1,000-2,000") == (
        "gb|accession|locus",
        1000,
        2000,
    )

    # Punctuation in names (aside from :)
    assert parse_region("name-with-hyphens-") == ("name-with-hyphens-", 0, None,)
    assert parse_region("GL000207.1") == ("GL000207.1", 0, None)
    assert parse_region("GL000207.1:1000-2000") == ("GL000207.1", 1000, 2000)

    # Trailing dash
    assert parse_region("chr21:1000-") == ("chr21", 1000, None)

    # Humanized units
    assert parse_region("6:1kb-2kb") == ("6", 1000, 2000)
    assert parse_region("6:1k-2000") == ("6", 1000, 2000)
    assert parse_region("6:1kb-2M") == ("6", 1000, 2000000)
    assert parse_region("6:1Gb-") == ("6", 1000000000, None)

    with pytest.raises(ValueError):
        parse_region("chr1:2,000-1,000")  # reverse selection
        parse_region("chr1::1000-2000")  # more than one colon

mirnylab / bioframe / tests / test_region.py View on Github

def test_parse_region():
    # UCSC-style names
    assert parse_region("chr21") == ("chr21", 0, None)
    assert parse_region("chr21:1000-2000") == ("chr21", 1000, 2000)
    assert parse_region("chr21:1,000-2,000") == ("chr21", 1000, 2000)

    # Ensembl style names
    assert parse_region("6") == ("6", 0, None)
    assert parse_region("6:1000-2000") == ("6", 1000, 2000)
    assert parse_region("6:1,000-2,000") == ("6", 1000, 2000)

    # FASTA style names
    assert parse_region("gb|accession|locus") == ("gb|accession|locus", 0, None,)
    assert parse_region("gb|accession|locus:1000-2000") == (
        "gb|accession|locus",
        1000,
        2000,
    )
    assert parse_region("gb|accession|locus:1,000-2,000") == (
        "gb|accession|locus",
        1000,
        2000,
    )

    # Punctuation in names (aside from :)

mirnylab / bioframe / tests / test_region.py View on Github

def test_parse_region():
    # UCSC-style names
    assert parse_region("chr21") == ("chr21", 0, None)
    assert parse_region("chr21:1000-2000") == ("chr21", 1000, 2000)
    assert parse_region("chr21:1,000-2,000") == ("chr21", 1000, 2000)

    # Ensembl style names
    assert parse_region("6") == ("6", 0, None)
    assert parse_region("6:1000-2000") == ("6", 1000, 2000)
    assert parse_region("6:1,000-2,000") == ("6", 1000, 2000)

    # FASTA style names
    assert parse_region("gb|accession|locus") == ("gb|accession|locus", 0, None,)
    assert parse_region("gb|accession|locus:1000-2000") == (
        "gb|accession|locus",
        1000,
        2000,
    )
    assert parse_region("gb|accession|locus:1,000-2,000") == (
        "gb|accession|locus",
        1000,

mirnylab / bioframe / tests / test_region.py View on Github

"gb|accession|locus",
        1000,
        2000,
    )

    # Punctuation in names (aside from :)
    assert parse_region("name-with-hyphens-") == ("name-with-hyphens-", 0, None,)
    assert parse_region("GL000207.1") == ("GL000207.1", 0, None)
    assert parse_region("GL000207.1:1000-2000") == ("GL000207.1", 1000, 2000)

    # Trailing dash
    assert parse_region("chr21:1000-") == ("chr21", 1000, None)

    # Humanized units
    assert parse_region("6:1kb-2kb") == ("6", 1000, 2000)
    assert parse_region("6:1k-2000") == ("6", 1000, 2000)
    assert parse_region("6:1kb-2M") == ("6", 1000, 2000000)
    assert parse_region("6:1Gb-") == ("6", 1000000000, None)

    with pytest.raises(ValueError):
        parse_region("chr1:2,000-1,000")  # reverse selection
        parse_region("chr1::1000-2000")  # more than one colon

mirnylab / bioframe / tests / test_region.py View on Github

assert parse_region("gb|accession|locus:1,000-2,000") == (
        "gb|accession|locus",
        1000,
        2000,
    )

    # Punctuation in names (aside from :)
    assert parse_region("name-with-hyphens-") == ("name-with-hyphens-", 0, None,)
    assert parse_region("GL000207.1") == ("GL000207.1", 0, None)
    assert parse_region("GL000207.1:1000-2000") == ("GL000207.1", 1000, 2000)

    # Trailing dash
    assert parse_region("chr21:1000-") == ("chr21", 1000, None)

    # Humanized units
    assert parse_region("6:1kb-2kb") == ("6", 1000, 2000)
    assert parse_region("6:1k-2000") == ("6", 1000, 2000)
    assert parse_region("6:1kb-2M") == ("6", 1000, 2000000)
    assert parse_region("6:1Gb-") == ("6", 1000000000, None)

    with pytest.raises(ValueError):
        parse_region("chr1:2,000-1,000")  # reverse selection
        parse_region("chr1::1000-2000")  # more than one colon

mirnylab / bioframe / tests / test_region.py View on Github

def test_parse_region():
    # UCSC-style names
    assert parse_region("chr21") == ("chr21", 0, None)
    assert parse_region("chr21:1000-2000") == ("chr21", 1000, 2000)
    assert parse_region("chr21:1,000-2,000") == ("chr21", 1000, 2000)

    # Ensembl style names
    assert parse_region("6") == ("6", 0, None)
    assert parse_region("6:1000-2000") == ("6", 1000, 2000)
    assert parse_region("6:1,000-2,000") == ("6", 1000, 2000)

    # FASTA style names
    assert parse_region("gb|accession|locus") == ("gb|accession|locus", 0, None,)
    assert parse_region("gb|accession|locus:1000-2000") == (
        "gb|accession|locus",
        1000,
        2000,
    )
    assert parse_region("gb|accession|locus:1,000-2,000") == (
        "gb|accession|locus",
        1000,
        2000,
    )

    # Punctuation in names (aside from :)
    assert parse_region("name-with-hyphens-") == ("name-with-hyphens-", 0, None,)

How to use bioframe - 10 common examples

To help you get started, we’ve selected a few bioframe examples, based on popular ways it is used in public projects.

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