def test_junction_extraction_from_splitmap():
input = files.open(testfiles["reads_1.fastq"])
index = testfiles["genome.gem"]
gtf_junctions = set(junctions.from_gtf(testfiles["refseq.gtf"]))
jj = gem.extract_junctions(input, index, merge_with=gtf_junctions)
assert junctions is not None
assert len(jj) == 260
def test_junction_extraction_from_splitmap():
input = files.open(testfiles["reads_1.fastq"])
index = testfiles["genome.gem"]
gtf_junctions = set(junctions.from_gtf(testfiles["refseq.gtf"]))
jj = gem.extract_junctions(input, index, merge_with=gtf_junctions)
assert junctions is not None
assert len(jj) == 260
def test_junction_extraction_from_gtf():
gtf_junctions = list(junctions.from_gtf(testfiles["refseq.gtf"]))
assert len(gtf_junctions) == 260
junctions.write_junctions(gtf_junctions, results_dir + "/annotation.junctions")
## reread the junctions
reread = junctions.from_junctions(results_dir + "/annotation.junctions")
assert reread is not None
assert len(reread) == 260
assert len(set(gtf_junctions).intersection(set(reread))) == 260
## merge junctions
merged = junctions.merge_junctions([gtf_junctions, reread])
assert merged is not None
assert len(merged) == 260
def test_junction_extraction_from_gtf():
gtf_junctions = list(junctions.from_gtf(testfiles["refseq.gtf"]))
assert len(gtf_junctions) == 260
junctions.write_junctions(gtf_junctions,
results_dir + "/annotation.junctions")
## reread the junctions
reread = junctions.from_junctions(results_dir + "/annotation.junctions")
assert reread is not None
assert len(reread) == 260
assert len(set(gtf_junctions).intersection(set(reread))) == 260
## merge junctions
merged = junctions.merge_junctions([gtf_junctions, reread])
assert merged is not None
assert len(merged) == 260
