def test_slopper(self):
loaded_bed = Bedfile(self.unsortedbed, "tests/data/getfasta.gt")
total_peaks = loaded_bed.get_total_peaks
train_bed_file, test_bed_file = loaded_bed.split_train_test_bed(
train_peaks_count=total_peaks / 2.0, test_peaks_count=total_peaks / 2.0
)
assert filecmp.cmp("tests/data/unsorted.train", "tests/data/expected_out/unsorted.train")
def test_traintest(self):
bedfile = "tests/data/ENCSR000AKB/ENCFF002CDP_1000_unsorted.bed"
loaded_bed = Bedfile(bedfile, self.genome_table, "tests/data/generated_out")
total_peaks = loaded_bed.get_total_peaks
train_bed_file, test_bed_file = loaded_bed.split_train_test_bed(
train_peaks_count=total_peaks / 2.0, test_peaks_count=total_peaks / 2.0
)
assert filecmp.cmp(
"tests/data/generated_out/ENCFF002CDP_1000_unsorted.train",
"tests/data/expected_out/ENCFF002CDP_1000_unsorted.train",
)
def test_generatefasta(self):
"""Test generate fasta"""
loaded_bed = Bedfile(self.getfastapeak, "tests/data/getfasta.gt")
total_peaks = loaded_bed.get_total_peaks
train_bed_file, test_bed_file = loaded_bed.split_train_test_bed(
train_peaks_count=total_peaks / 2.0, test_peaks_count=total_peaks / 2.0
)
train_slopped = loaded_bed.slop_bed(train_bed_file, flank_length=20)
# test_sloppped = loaded_bed.slop_bed(test_bed_file, flank_length=20)
train_fasta_out = loaded_bed.extract_fasta(
bed_in=train_slopped, fasta_in="tests/data/getfasta.fa", fasta_out="tests/data/generated_out/getfasta.fa"
)
assert filecmp.cmp("tests/data/generated_out/getfasta.fa", "tests/data/expected_out/getfasta.fa")
