How to use the bioframe.digest 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.
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mirnylab / bioframe / tests / test_genomeops.py View on Github 
def test_digest():
pytest.importorskip("Bio")
fasta_records = bioframe.load_fasta(testdir+"/test_data/test.fa")
assert len(fasta_records) == 2
### no HindIII sites in the test.fa fasta records, so shouldn't change shape[0]
assert bioframe.digest(fasta_records, "HindIII").shape == (2, 3)
### one DpnII site on chrTEST2, shape[0] should increase by one
assert bioframe.digest(fasta_records, "DpnII").shape == (3, 3)
### DpnII site is on chrTEST2 position 3, first interval of chrTEST2 should end at 3
assert bioframe.digest(fasta_records, "DpnII").iloc[1].end == 3def test_digest():
pytest.importorskip("Bio")
fasta_records = bioframe.load_fasta(testdir+"/test_data/test.fa")
assert len(fasta_records) == 2
### no HindIII sites in the test.fa fasta records, so shouldn't change shape[0]
assert bioframe.digest(fasta_records, "HindIII").shape == (2, 3)
### one DpnII site on chrTEST2, shape[0] should increase by one
assert bioframe.digest(fasta_records, "DpnII").shape == (3, 3)
### DpnII site is on chrTEST2 position 3, first interval of chrTEST2 should end at 3
assert bioframe.digest(fasta_records, "DpnII").iloc[1].end == 3def test_digest():
pytest.importorskip("Bio")
fasta_records = bioframe.load_fasta(testdir+"/test_data/test.fa")
assert len(fasta_records) == 2
### no HindIII sites in the test.fa fasta records, so shouldn't change shape[0]
assert bioframe.digest(fasta_records, "HindIII").shape == (2, 3)
### one DpnII site on chrTEST2, shape[0] should increase by one
assert bioframe.digest(fasta_records, "DpnII").shape == (3, 3)
### DpnII site is on chrTEST2 position 3, first interval of chrTEST2 should end at 3
assert bioframe.digest(fasta_records, "DpnII").iloc[1].end == 3bioframe
Operations and utilities for Genomic Interval Dataframes.
Package Health Score
81 / 100Popular bioframe functions
- bioframe._process.run
- bioframe._process.tsv
- bioframe._region.parse_region
- bioframe.arrops.stack_intervals
- bioframe.binnify
- bioframe.closest
- bioframe.cluster
- bioframe.coverage
- bioframe.digest
- bioframe.formats.read_chromsizes
- bioframe.formats.read_table
- bioframe.frac_mapped
- bioframe.load_fasta
- bioframe.merge
- bioframe.ops._verify_columns
- bioframe.overlap
- bioframe.read_chromsizes
- bioframe.region.parse_region
- bioframe.select
- bioframe.subtract