def test_find_nearest_BRAF_exon(ensembl):
braf = ensembl.genes_by_name("BRAF")[0]
braf_transcripts = braf.transcripts
exons = braf_transcripts[0].exons
for exon in exons:
# immediately before exon
result_before = find_nearest_locus(
start=exon.start - 2,
end=exon.start - 1,
loci=exons)
eq_(result_before, (1, exon))
# overlapping with exon
result_overlap = find_nearest_locus(
start=exon.start - 2,
end=exon.start + 1,
loci=exons)
eq_(result_overlap, (0, exon))
# immediately after exon
result_after = find_nearest_locus(
start=exon.end + 1,
end=exon.end + 2,
loci=exons)
eq_(result_after, (1, exon))
def test_find_nearest_BRAF_transcript(ensembl):
braf_transcript = ensembl.transcripts_by_name("BRAF-001")[0]
egfr_transcript = ensembl.transcripts_by_name("EGFR-001")[0]
transcripts = [braf_transcript, egfr_transcript]
for transcript in transcripts:
# immediately before transcript
result_before = find_nearest_locus(
start=transcript.start - 2,
end=transcript.start - 1,
loci=transcripts)
eq_(result_before, (1, transcript))
# overlapping with transcript
result_overlap = find_nearest_locus(
start=transcript.start - 2,
end=transcript.start + 1,
loci=transcripts)
eq_(result_overlap, (0, transcript))
# immediately after transcript
# may overlap with other transcripts
result_after = find_nearest_locus(
start=transcript.end + 1,
end=transcript.end + 2,
loci=transcripts)
eq_(result_after, (1, transcript))
def test_find_nearest_BRAF_exon(ensembl):
braf = ensembl.genes_by_name("BRAF")[0]
braf_transcripts = braf.transcripts
exons = braf_transcripts[0].exons
for exon in exons:
# immediately before exon
result_before = find_nearest_locus(start=exon.start - 2,
end=exon.start - 1,
loci=exons)
eq_(result_before, (1, exon))
# overlapping with exon
result_overlap = find_nearest_locus(start=exon.start - 2,
end=exon.start + 1,
loci=exons)
eq_(result_overlap, (0, exon))
# immediately after exon
result_after = find_nearest_locus(start=exon.end + 1,
end=exon.end + 2,
loci=exons)
eq_(result_after, (1, exon))
def test_find_nearest_BRAF_transcript(ensembl):
braf_transcript = ensembl.genes_by_name("BRAF")[0].transcripts[0]
egfr_transcript = ensembl.genes_by_name("EGFR")[0].transcripts[0]
transcripts = [braf_transcript, egfr_transcript]
for transcript in transcripts:
# immediately before transcript
result_before = find_nearest_locus(start=transcript.start - 2,
end=transcript.start - 1,
loci=transcripts)
eq_(result_before, (1, transcript))
# overlapping with transcript
result_overlap = find_nearest_locus(start=transcript.start - 2,
end=transcript.start + 1,
loci=transcripts)
eq_(result_overlap, (0, transcript))
# immediately after transcript
# may overlap with other transcripts
result_after = find_nearest_locus(start=transcript.end + 1,
end=transcript.end + 2,
loci=transcripts)
eq_(result_after, (1, transcript))
