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from deeptoolsintervals import GTF
from deeptoolsintervals import Enrichment
# Very basic test to check functionality
def test_functionality():
gtf = GTF(["GRCh38.84.2.gtf.gz", "GRCh38.84.bed", "GRCh38.84.gtf.gz"], keepExons=True)
list_labels = gtf.labels
list_labels.sort()
assert(list_labels == ['GRCh38.84.2.gtf.gz', 'GRCh38.84.bed', 'GRCh38.84.gtf.gz', 'group 1', 'group 1_r1', 'group 2', 'group 3', 'group2'])
gtf = GTF("GRCh38.84.gtf.gz", keepExons=True)
assert(gtf.findOverlaps("chr1", 1, 20000)[0][0] >= 11800)
gtf = Enrichment("GRCh38.84.gtf.gz", keepExons=True, attributeKey="gene_biotype")
overlap_result = list(gtf.findOverlaps("1", [(0, 2000000)]))
overlap_result.sort()
assert(overlap_result ==
['group 1', 'group 2', 'lincRNA', 'miRNA', 'processed_pseudogene', 'protein_coding', 'transcribed_unprocessed_pseudogene', 'unprocessed_pseudogene'])
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