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")