1. Advisor
  2. bioframe
  3. functions
  4. bioframe._region.parse_region
View all bioframe analysis

How to use the bioframe._region.parse_region function in bioframe

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

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github mirnylab / bioframe / tests / test_region.py View on Github external
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",
github mirnylab / bioframe / tests / test_region.py View on Github external
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
github mirnylab / bioframe / tests / test_region.py View on Github external
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
github mirnylab / bioframe / tests / test_region.py View on Github external
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
github mirnylab / bioframe / tests / test_region.py View on Github external
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
github mirnylab / bioframe / tests / test_region.py View on Github external
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 :)
github mirnylab / bioframe / tests / test_region.py View on Github external
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,
github mirnylab / bioframe / tests / test_region.py View on Github external
"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
github mirnylab / bioframe / tests / test_region.py View on Github external
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
github mirnylab / bioframe / tests / test_region.py View on Github external
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,)

bioframe

Operations and utilities for Genomic Interval Dataframes.

GitHub
MIT
Latest version published 6 months ago

Package Health Score

69 / 100
Full package analysis

Popular bioframe functions

Similar packages