diff --git a/src/gc_content/gc_content.py b/src/gc_content/gc_content.py index 0ffe299c8a6a7dd9ac2dd73a3833609dc8a46532..b34e87184168e2f2ac3bc0d784f9b77f4736a1c4 100644 --- a/src/gc_content/gc_content.py +++ b/src/gc_content/gc_content.py @@ -29,24 +29,26 @@ def get_gc_content(bed_line: List[Any], dic_seq: Fasta) -> float: :param dic_seq: A dictionary containing chromosomal sequences :return: The gc content + >>> dic_seq = Fasta(str(TestConfig.test_fasta)) >>> get_gc_content(["chr1", 0, 10, "s1", ".", "+"], - ... Fasta(str(TestConfig.test_fasta))) + ... dic_seq) 100.0 >>> get_gc_content(["chr1", 10, 20, "s1", ".", "+"], - ... Fasta(str(TestConfig.test_fasta))) + ... dic_seq) 50.0 >>> get_gc_content(["chr1", 20, 30, "s1", ".", "+"], - ... Fasta(str(TestConfig.test_fasta))) + ... dic_seq) 0.0 >>> get_gc_content(["chr1", 0, 10, "s1", ".", "-"], - ... Fasta(str(TestConfig.test_fasta))) + ... dic_seq) 100.0 >>> get_gc_content(["chr1", 10, 20, "s1", ".", "-"], - ... Fasta(str(TestConfig.test_fasta))) + ... dic_seq) 50.0 >>> get_gc_content(["chr1", 20, 30, "s1", ".", "-"], - ... Fasta(str(TestConfig.test_fasta))) + ... dic_seq) 0.0 + >>> dic_seq.close() """ seq = str(dic_seq[bed_line[0]][bed_line[1]:bed_line[2]]).upper() if "N" in seq: @@ -69,15 +71,17 @@ def get_many_gc_content(bed_line: List[Any], dic_seq: Fasta, :return: A dictionary containing the GC content inside the interval \ we want to get and around it. + >>> dic_seq = Fasta(str(TestConfig.test_fasta)) >>> get_many_gc_content(["chr1", 10, 20, "s1", ".", "+"], - ... Fasta(str(TestConfig.test_fasta)), 0) + ... dic_seq, 0) {'interval': 50.0} >>> get_many_gc_content(["chr1", 10, 20, "s1", ".", "+"], - ... Fasta(str(TestConfig.test_fasta)), 10) + ... dic_seq, 10) {'before': 100.0, 'interval': 50.0, 'after': 0.0} >>> get_many_gc_content(["chr1", 10, 20, "s1", ".", "-"], - ... Fasta(str(TestConfig.test_fasta)), 10) + ... dic_seq, 10) {'before': 0.0, 'interval': 50.0, 'after': 100.0} + >>> dic_seq.close() """ gc_interval = get_gc_content(bed_line, dic_seq) if environment == 0: