def construct_gene_object(ensembl, transcript_id):
""" creates an Transcript object for a gene from ensembl databases
Args:
ensembl: EnsemblRequest object to request data from ensembl
transcript_id: string for an Ensembl transcript ID
Returns:
a Transcript object, containing transcript coordinates and gene and
transcript sequence.
Raises:
ValueError if CDS from genomic sequence given gene coordinates and CDS
retrieved from Ensembl do not match.
"""
# get the sequence for the identified transcript
(chrom, start, end, strand,
genomic_sequence) = ensembl.get_genomic_seq_for_transcript(transcript_id,
expand=10)
cds_sequence = ensembl.get_cds_seq_for_transcript(transcript_id)
# get the locations of the exons and cds from ensembl
cds_ranges = ensembl.get_cds_ranges_for_transcript(transcript_id)
exon_ranges = ensembl.get_exon_ranges_for_transcript(transcript_id)
# start a Transcript object with the locations and sequence
transcript = Transcript(transcript_id, chrom, start, end, strand)
transcript.set_exons(exon_ranges, cds_ranges)
transcript.set_cds(cds_ranges)
transcript.add_cds_sequence(cds_sequence)
transcript.add_genomic_sequence(genomic_sequence, offset=10)
return transcript
def test_set_cds(self):
""" test that set_cds() works correctly
"""
exons = [(0, 200), (800, 1000)]
cds = [(100, 200), (800, 900)]
# make sure we raise an error if we try to set the CDS before the exons
with self.assertRaises(ValueError):
tx = Transcript('test', '1', 0, 1000, '+')
tx.set_cds(cds)
# check CDS positions
self.gene.set_exons(exons, cds)
self.gene.set_cds(cds)
self.assertEqual(self.gene.get_cds(), [{'start': 100, 'end': 200}, {'start': 800, 'end': 900}])
# check that CDS ends outside an exon are corrected
exons = [(0, 200), (300, 400), (800, 1000)]
cds = [(100, 200), (300, 402)]
self.gene.set_exons(exons, cds)
self.gene.set_cds(cds)
self.assertEqual(self.gene.get_cds(), [{'start': 100, 'end': 200},
{'start': 300, 'end': 400}, {'start': 800, 'end': 802}])
cds = [(298, 400), (800, 1000)]
self.gene.set_exons(exons, cds)
self.gene.set_cds(cds)
self.assertEqual(self.gene.get_cds(), [{'start': 198, 'end': 200},
{'start': 300, 'end': 400}, {'start': 800, 'end': 1000}])
async def construct_gene_object(ensembl, transcript_id):
""" creates an Transcript object for a gene from ensembl databases
Args:
ensembl: EnsemblRequest object to request data from ensembl
transcript_id: string for an Ensembl transcript ID
Returns:
a Transcript object, containing transcript coordinates and gene and
transcript sequence.
Raises:
ValueError if CDS from genomic sequence given gene coordinates and CDS
retrieved from Ensembl do not match.
"""
tasks = [
get_genomic_seq_for_transcript(ensembl, transcript_id, expand=10),
get_cds_seq_for_transcript(ensembl, transcript_id),
get_cds_ranges_for_transcript(ensembl, transcript_id),
get_exon_ranges_for_transcript(ensembl, transcript_id)
]
(chrom, start, end, strand,
genomic), cds_seq, cds, exons = await asyncio.gather(*tasks)
# start a Transcript object with the locations and sequence
transcript = Transcript(transcript_id, chrom, start, end, strand)
transcript.set_exons(exons, cds)
transcript.set_cds(cds)
transcript.add_cds_sequence(cds_seq)
transcript.add_genomic_sequence(genomic, offset=10)
return transcript
def construct_gene(self, name='TEST', chrom='1', start=100, end=179,
strand='+', exons=[(100, 119), (160, 179)],
cds=[(110, 119), (160, 170)]):
tx = Transcript(name, chrom, start, end, strand)
tx.set_exons(exons, cds)
tx.set_cds(cds)
return tx
def construct_gene_object(ensembl, transcript_id):
""" creates an Transcript object for a gene from ensembl databases
Args:
ensembl: EnsemblRequest object to request data from ensembl
transcript_id: string for an Ensembl transcript ID
Returns:
a Transcript object, containing transcript coordinates and gene and
transcript sequence.
Raises:
ValueError if CDS from genomic sequence given gene coordinates and CDS
retrieved from Ensembl do not match.
"""
# get the sequence for the identified transcript
(chrom, start, end, strand, genomic_sequence) = ensembl.get_genomic_seq_for_transcript(transcript_id, expand=10)
cds_sequence = ensembl.get_cds_seq_for_transcript(transcript_id)
# get the locations of the exons and cds from ensembl
cds_ranges = ensembl.get_cds_ranges_for_transcript(transcript_id)
exon_ranges = ensembl.get_exon_ranges_for_transcript(transcript_id)
# start a Transcript object with the locations and sequence
transcript = Transcript(transcript_id, chrom, start, end, strand)
transcript.set_exons(exon_ranges, cds_ranges)
transcript.set_cds(cds_ranges)
transcript.add_cds_sequence(cds_sequence)
transcript.add_genomic_sequence(genomic_sequence, offset=10)
return transcript
def test_merge_coordinates(self):
""" test that we can merge transcripts with odd overlaps
"""
a = Transcript("a", "1", 10, 20, "+")
exons1 = [{'start': 10, 'end': 20}, {'start': 25, 'end': 40}]
exons2 = [{'start': 10, 'end': 30}]
self.assertEqual(a.merge_coordinates(exons1, exons2),
a.merge_coordinates(exons2, exons1))
def test_add_genomic_sequencE_without_cds_coords(self):
""" test that error is raised if we add gDNA without CDS coords
"""
a = Transcript("a", "1", 10, 20, "+")
a.set_exons([(10, 20)], [(10, 20)])
with self.assertRaises(ValueError):
a.add_genomic_sequence('CGTAGACTGTACGCATCGATT', offset=5)
a.set_cds([(10, 20)])
a.add_genomic_sequence('CGTAGACTGTACGCATCGATT', offset=5)
def test_fix_cds_boundary(self):
""" test that _fix_out_of_exon_cds_boundary() works correctly
"""
exons = [(1100, 1200), (1300, 1400), (1800, 1900)]
cds = [(1300, 1400)]
tx = Transcript('test', '1', 0, 1000, '+')
tx.set_exons(exons, cds)
self.assertEqual(tx.fix_cds_boundary(1295), {
'start': 1195,
'end': 1200
})
self.assertEqual(tx.fix_cds_boundary(1205), {
'start': 1300,
'end': 1305
})
self.assertEqual(tx.fix_cds_boundary(1402), {
'start': 1800,
'end': 1802
})
self.assertEqual(tx.fix_cds_boundary(1798), {
'start': 1398,
'end': 1400
})
# raise an error if the position is within the exons
with self.assertRaises(ValueError):
self.gene.fix_cds_boundary(1105)
def test_add_genomic_sequencE_without_cds_coords(self):
""" test that error is raised if we add gDNA without CDS coords
"""
a = Transcript("a", "1", 10, 20, "+")
a.set_exons([(10, 20)], [(10, 20)])
with self.assertRaises(ValueError):
a.add_genomic_sequence('CGTAGACTGTACGCATCGATT', offset=5)
a.set_cds([(10, 20)])
a.add_genomic_sequence('CGTAGACTGTACGCATCGATT', offset=5)
def construct_gene(self):
chrom = "1"
name = "TEST"
strand = "+"
start = 0
end = 70
exons = [(5, 58)]
cds = [(5, 58)]
transcript = Transcript(name, chrom, start, end, strand)
transcript.set_exons(exons, cds)
transcript.set_cds(cds)
cds = "ATGTGGGCTCCACCAGCAGCAATCATGGGATGGGCCCACCAAGAAGGTGGGTAA"
gdna = "GGGGGATGTGGGCTCCACCAGCAGCAATCATGGGATGGGCCCACCAAGAAGGTGGGTAACCAGGCCCC"
transcript.add_cds_sequence(cds)
transcript.add_genomic_sequence(gdna)
return transcript
def test_fix_cds_boundary(self):
""" test that _fix_out_of_exon_cds_boundary() works correctly
"""
exons = [(1100, 1200), (1300, 1400), (1800, 1900)]
cds = [(1300, 1400)]
tx = Transcript('test', '1', 0, 1000, '+')
tx.set_exons(exons, cds)
self.assertEqual(tx.fix_cds_boundary(1295), {'start': 1195, 'end': 1200})
self.assertEqual(tx.fix_cds_boundary(1205), {'start': 1300, 'end': 1305})
self.assertEqual(tx.fix_cds_boundary(1402), {'start': 1800, 'end': 1802})
self.assertEqual(tx.fix_cds_boundary(1798), {'start': 1398, 'end': 1400})
# raise an error if the position is within the exons
with self.assertRaises(ValueError):
self.gene.fix_cds_boundary(1105)
def test_get_de_novos_in_transcript(self):
""" test that we can identify de novos within the CDS of a transcript
"""
exon_ranges = [(10, 20), (30, 40), (90, 100)]
cds_ranges = [(30, 40), (90, 95)]
# define a simple transcript
tx = Transcript("test1", '1', 10, 100, "+")
tx.set_exons(exon_ranges, cds_ranges)
tx.set_cds(cds_ranges)
# check that only the site in the CDS is returned
sites = [15, 35, 100]
self.assertEqual(get_de_novos_in_transcript(tx, sites), [35])
# check that we can return multiple sites in the CDS
sites = [15, 35, 90]
self.assertEqual(get_de_novos_in_transcript(tx, sites), [35, 90])
# check if we pass in an empty list, we get one back
self.assertEqual(get_de_novos_in_transcript(tx, []), [])
def construct_gene(self, name='TEST', chrom='1', start=1000, end=2000,
strand='+', exons=[(1000, 1200), (1800, 2000)],
cds=[(1100, 1200), (1800, 1900)]):
tx = Transcript(name, chrom, start, end, strand)
tx.set_exons(exons, cds)
tx.set_cds(cds)
return tx
def construct_gene(self,
name='TEST',
chrom='1',
start=100,
end=179,
strand='+',
exons=[(100, 119), (160, 179)],
cds=[(110, 119), (160, 170)]):
tx = Transcript(name, chrom, start, end, strand)
tx.set_exons(exons, cds)
tx.set_cds(cds)
return tx
def test_get_de_novos_in_transcript(self):
""" test that we can identify de novos within the CDS of a transcript
"""
exon_ranges = [(10, 20), (30, 40), (90, 100)]
cds_ranges = [(30, 40), (90, 95)]
# define a simple transcript
tx = Transcript("test1", '1', 10, 100, "+")
tx.set_exons(exon_ranges, cds_ranges)
tx.set_cds(cds_ranges)
# check that only the site in the CDS is returned
sites = [15, 35, 100]
self.assertEqual(get_de_novos_in_transcript(tx, sites), [35])
# check that we can return multiple sites in the CDS
sites = [15, 35, 90]
self.assertEqual(get_de_novos_in_transcript(tx, sites), [35, 90])
# check if we pass in an empty list, we get one back
self.assertEqual(get_de_novos_in_transcript(tx, []), [])
def test___add__cds_length_fixed(self):
""" check that we can merge transcripts, even with fixed CDS coords
"""
a = Transcript("a", "1", 10, 20, "+")
a.set_exons([(10, 20)], [(10, 20)])
a.set_cds([(10, 20)])
a.add_cds_sequence('ACTGTACGCAT')
a.add_genomic_sequence('CGTAGACTGTACGCATCGATT', offset=5)
b = Transcript("b", "1", 0, 10, "+")
b.set_exons([(0, 10)], [(0, 10)])
b.set_cds([(0, 10)])
b.add_cds_sequence('ACTGTACGCAT')
b.add_genomic_sequence('CGTAGACTGTACGCATCGTAG', offset=5)
# without a fix to tx.cpp to adjust an exon coordinate simultaneously,
# the line below would give an error.
c = a + b
def test___add__not_overlapping(self):
''' test that __add__() works correctly when transcripts do not overlap
'''
a = Transcript("a", "1", 10, 50, "+")
b = Transcript("b", "1", 60, 80, "+")
a.set_exons([(10, 50)], [(10, 50)])
a.set_cds([(10, 50)])
a.add_genomic_sequence('N' * 40)
b.set_exons([(60, 80)], [(60, 80)])
b.set_cds([(60, 80)])
b.add_genomic_sequence('N' * 20)
self.assertEqual(len((a + b).get_genomic_sequence()), 70)
def test___add__(self):
""" test that __add__() works correctly
"""
exons = [(10, 20), (50, 60), (90, 100)]
cds_2 = [(50, 60), (90, 95)]
a = Transcript("a", "1", 10, 100, "+")
b = Transcript("b", "1", 10, 100, "+")
c = Transcript("c", "1", 10, 100, "+")
d = Transcript("d", "1", 10, 100, "+")
a.set_exons(exons, [(55, 60), (90, 100)])
a.set_cds([(55, 60), (90, 100)])
b.set_exons(exons, [(50, 60), (90, 95)])
b.set_cds([(50, 60), (90, 95)])
c.set_exons([(45, 65)], [(45, 65)])
c.set_cds([(45, 65)])
d.set_exons([(30, 40)], [(30, 40)])
d.set_cds([(30, 40)])
# check that adding two Transcripts gives the union of CDS regions
self.assertEqual((a + b).get_cds(), [{'start': 50, 'end': 60}, {'start': 90, 'end': 100}])
self.assertEqual((a + c).get_cds(), [{'start': 45, 'end': 65}, {'start': 90, 'end': 100}])
# check that addition is reversible
self.assertEqual((c + a).get_cds(), [{'start': 45, 'end': 65}, {'start': 90, 'end': 100}])
# check that adding previously unknown exons works
self.assertEqual((a + d).get_cds(), [{'start': 30, 'end': 40}, {'start': 55, 'end': 60}, {'start': 90, 'end': 100}])
# check that we can add transcript + None correctly
self.assertEqual(a + None, a)
self.assertEqual(None + a, a)
def set_transcript(self):
""" construct a transcript for a known gene
"""
exon_ranges=[(120933859, 120934019), (120934219, 120934356),
(120935876, 120936296)]
cds_ranges=[(120934225, 120934356), (120935876, 120936013)]
expected = Transcript("ENST00000242577", '12', 120933859, 120936296, "+")
expected.set_exons(exon_ranges, cds_ranges)
expected.set_cds(cds_ranges)
cds = "ATGTGCGACCGAAAGGCCGTGATCAAAAATGCGGACATGTCGGAAGAGATGCAACAGGACTC" \
"GGTGGAGTGCGCTACTCAGGCGCTGGAGAAATACAACATAGAGAAGGACATTGCGGCTCATATC" \
"AAGAAGGAATTTGACAAGAAGTACAATCCCACCTGGCATTGCATCGTGGGGAGGAACTTCGGTA" \
"GTTATGTGACACATGAAACCAAACACTTCATCTACTTCTACCTGGGCCAAGTGGCCATTCTTCT" \
"GTTCAAATCTGGTTAA"
genomic = "GGGCGGGGCCGGCGGGAGCAGGGCGGGGCCTGAGCACTAGGCGGCGGCGGCTGGCGTGGG" \
"GCTGCTTAGATGCGCCACGGTTTCGGTAGCGACGGTATCTCTAGCCGGGCCTGAGCTGTGCTAGCA" \
"CCTCCCCCAGGAGACCGTTGCAGTCGGCCAGCCCCCTTCTCCACGGTGAGAAACTCGGGGGGCCAG" \
"GGGGTGTCCTCGCTGCCTTATTTCGCCCCACTCCGGACTTAGCCCTCCGCGTAGCCCGCGCTTCCT" \
"GAGAAGTGGGGTGGGGGGCGTCGTCCCGTGGTGGCGCCGGCCGGGGTGGGGGCAGTTAGTGCCTGG" \
"GGGGCGCGGCCCAACTCAACCCCTTACCCCAGGCCTTGCCCACTAGGTAACCATGTGCGACCGAAA" \
"GGCCGTGATCAAAAATGCGGACATGTCGGAAGAGATGCAACAGGACTCGGTGGAGTGCGCTACTCA" \
"GGCGCTGGAGAAATACAACATAGAGAAGGACATTGCGGCTCATATCAAGAAGGTGAGGATGGGCGC" \
"GGGGGCCGATACGCAGCCGGGAGCAGGGGGTTCCTTCCCCCCGATCCTGCTTTCCTAAGGGCGCCT" \
"GACAGGTCCCGGGAATACTGCTGGCGGCTTGGGGCGTAGAAGCTTCCAGAAAGGACGCAGATGCAT" \
"TTTGCGCTCCTGTGGAGAAGACCAGACCCCCGGCGTCCGAAGTTTTTTTTTTTTTTTTTTTAATTA" \
"CCCAGCTCCGCGGGGGGAAAGCGCCACCTAGCAACGGTATCTAAGATCAGGGAGCAGCGGTTCCCC" \
"CTTCTGTGTGGTTCCTGCGCCGAGGATCCATCTGGGTGTTCCGGAGGGGGGAGCTGCGTGGGTGTT" \
"TCCAGCCGGGCCGGGAGGAGATCTTGCCAGCCTTCCAGTGGGGAGTTGAGGGAAGGTGGTGGGTGG" \
"TGGCGGGGCTGGGGGCTGGGGTAGGGGCTTGGTAAATGGCAGTCTAGAAAGCCGGCAGGACTGCCA" \
"ACTTCTCGAGCAGTGTTTGCTGGAAGGGAAGAAAGCTGGCAGCCTAAGCCGTGGGAGGGTTCCAGT" \
"CGAGAATGGGAAGATGAAAGACTTCAGATGGAACAGAAATAAATGCCTTTTTTGACAAACGCAGCA" \
"GTGCGTGCCTCTAGCTTGCAAGAGCGTTACTCCCCTTCATAGCTTTAAAAGGTTTTCGCACTGCGT" \
"GCAGTTAGAGTAGCTAAATCTTGTGTGACGCTCCACAAACACTTGTAAGAATTTTGCAGAGAAAGA" \
"TAACCGTTGCCACCCAATGCCCCCCACAGGCATTCTACTCCCCAGTACCTCTTAGGGTGGGAGAAA" \
"TGGTGAAGAGTTGTTCCTACAACTTGCTAACCTAGTGGACAGGGTAGTAGATTAGCATCATCCGGA" \
"TAGATGTGAAGAGGACGGCTGTTTGGATAATAATTAAGGATAAAATTTGGCCAGTTGACAGATTCT" \
"GTTTCCAGCAGTTTTTACAGCAACAGTGGAGTGCTTCAGTATTGTGTTCCTGTAAATTTAATTTTG" \
"ATCCGCAATCATTTGGTATACAATGCTGTTTGAAGTTTTGTCCTATTGGAAAAGTCTTGTGTTGCA" \
"GGGGTGCAGTTAAGATCTTTGTGATGAGGAATGGGATGGGCTAATTTTTTGCCGTTTTCTTGGAAT" \
"TGGGGGCATGGCAAATACAGTAGGGTAGTTTAGTTCTCTACACAGAACATGATAAACTACACCTGT" \
"TGATGTCACCGTCTGTCAATGAATATTATAGAAGGTATGAAGGTGTAATTACCATAATAACAAAAC" \
"ACCCTGTCTTTAGGGCTGACCTTTCGTCCTTTGACCTCCTCAGCCTCCATTCCCATCTTCGCTCAG" \
"ACTGCAAGTATGTTTGTATTAATGTACTATGTAGGCGGCTTGGAGCTGGGGAACATTCTTTCATTC" \
"TAAGAATTTGCAGATGCTGACGTTCCTCCTTTCTGCCCCTACAGGCTCTGGCTTATCCAAGAGGCA" \
"AACACTGACCTCTGGTAATTAAAATCCTAGTTCTTTTCTTTTGTCTTTTCCAGGAATTTGACAAGA" \
"AGTACAATCCCACCTGGCATTGCATCGTGGGGAGGAACTTCGGTAGTTATGTGACACATGAAACCA" \
"AACACTTCATCTACTTCTACCTGGGCCAAGTGGCCATTCTTCTGTTCAAATCTGGTTAAAAGCATG" \
"GACTGTGCCACACACCCAGTGATCCATCCAAAAACAAGGACTGCAGCCTAAATTCCAAATACCAGA" \
"GACTGAAATTTTCAGCCTTGCTAAGGGAACATCTCGATGTTTGAACCTTTGTTGTGTTTTGTACAG" \
"GGCATTCTCTGTACTAGTTTGTCGTGGTTATAAAACAATTAGCAGAATAGCCTACATTTGTATTTA" \
"TTTTCTATTCCATACTTCTGCCCACGTTGTTTTCTCTCAAAATCCATTCCTTTAAAAAATAAATCT" \
"GATGCAGATGTGTATGTGTGTG"
expected.add_cds_sequence(cds)
expected.add_genomic_sequence(genomic, offset=10)
return expected
def set_transcript(self):
""" construct a transcript for a known gene
"""
exon_ranges = [(120933859, 120934019), (120934219, 120934356),
(120935876, 120936296)]
cds_ranges = [(120934225, 120934356), (120935876, 120936013)]
expected = Transcript("ENST00000242577", '12', 120933859, 120936296,
"+")
expected.set_exons(exon_ranges, cds_ranges)
expected.set_cds(cds_ranges)
cds = "ATGTGCGACCGAAAGGCCGTGATCAAAAATGCGGACATGTCGGAAGAGATGCAACAGGACTC" \
"GGTGGAGTGCGCTACTCAGGCGCTGGAGAAATACAACATAGAGAAGGACATTGCGGCTCATATC" \
"AAGAAGGAATTTGACAAGAAGTACAATCCCACCTGGCATTGCATCGTGGGGAGGAACTTCGGTA" \
"GTTATGTGACACATGAAACCAAACACTTCATCTACTTCTACCTGGGCCAAGTGGCCATTCTTCT" \
"GTTCAAATCTGGTTAA"
genomic = "GGGCGGGGCCGGCGGGAGCAGGGCGGGGCCTGAGCACTAGGCGGCGGCGGCTGGCGTGGG" \
"GCTGCTTAGATGCGCCACGGTTTCGGTAGCGACGGTATCTCTAGCCGGGCCTGAGCTGTGCTAGCA" \
"CCTCCCCCAGGAGACCGTTGCAGTCGGCCAGCCCCCTTCTCCACGGTGAGAAACTCGGGGGGCCAG" \
"GGGGTGTCCTCGCTGCCTTATTTCGCCCCACTCCGGACTTAGCCCTCCGCGTAGCCCGCGCTTCCT" \
"GAGAAGTGGGGTGGGGGGCGTCGTCCCGTGGTGGCGCCGGCCGGGGTGGGGGCAGTTAGTGCCTGG" \
"GGGGCGCGGCCCAACTCAACCCCTTACCCCAGGCCTTGCCCACTAGGTAACCATGTGCGACCGAAA" \
"GGCCGTGATCAAAAATGCGGACATGTCGGAAGAGATGCAACAGGACTCGGTGGAGTGCGCTACTCA" \
"GGCGCTGGAGAAATACAACATAGAGAAGGACATTGCGGCTCATATCAAGAAGGTGAGGATGGGCGC" \
"GGGGGCCGATACGCAGCCGGGAGCAGGGGGTTCCTTCCCCCCGATCCTGCTTTCCTAAGGGCGCCT" \
"GACAGGTCCCGGGAATACTGCTGGCGGCTTGGGGCGTAGAAGCTTCCAGAAAGGACGCAGATGCAT" \
"TTTGCGCTCCTGTGGAGAAGACCAGACCCCCGGCGTCCGAAGTTTTTTTTTTTTTTTTTTTAATTA" \
"CCCAGCTCCGCGGGGGGAAAGCGCCACCTAGCAACGGTATCTAAGATCAGGGAGCAGCGGTTCCCC" \
"CTTCTGTGTGGTTCCTGCGCCGAGGATCCATCTGGGTGTTCCGGAGGGGGGAGCTGCGTGGGTGTT" \
"TCCAGCCGGGCCGGGAGGAGATCTTGCCAGCCTTCCAGTGGGGAGTTGAGGGAAGGTGGTGGGTGG" \
"TGGCGGGGCTGGGGGCTGGGGTAGGGGCTTGGTAAATGGCAGTCTAGAAAGCCGGCAGGACTGCCA" \
"ACTTCTCGAGCAGTGTTTGCTGGAAGGGAAGAAAGCTGGCAGCCTAAGCCGTGGGAGGGTTCCAGT" \
"CGAGAATGGGAAGATGAAAGACTTCAGATGGAACAGAAATAAATGCCTTTTTTGACAAACGCAGCA" \
"GTGCGTGCCTCTAGCTTGCAAGAGCGTTACTCCCCTTCATAGCTTTAAAAGGTTTTCGCACTGCGT" \
"GCAGTTAGAGTAGCTAAATCTTGTGTGACGCTCCACAAACACTTGTAAGAATTTTGCAGAGAAAGA" \
"TAACCGTTGCCACCCAATGCCCCCCACAGGCATTCTACTCCCCAGTACCTCTTAGGGTGGGAGAAA" \
"TGGTGAAGAGTTGTTCCTACAACTTGCTAACCTAGTGGACAGGGTAGTAGATTAGCATCATCCGGA" \
"TAGATGTGAAGAGGACGGCTGTTTGGATAATAATTAAGGATAAAATTTGGCCAGTTGACAGATTCT" \
"GTTTCCAGCAGTTTTTACAGCAACAGTGGAGTGCTTCAGTATTGTGTTCCTGTAAATTTAATTTTG" \
"ATCCGCAATCATTTGGTATACAATGCTGTTTGAAGTTTTGTCCTATTGGAAAAGTCTTGTGTTGCA" \
"GGGGTGCAGTTAAGATCTTTGTGATGAGGAATGGGATGGGCTAATTTTTTGCCGTTTTCTTGGAAT" \
"TGGGGGCATGGCAAATACAGTAGGGTAGTTTAGTTCTCTACACAGAACATGATAAACTACACCTGT" \
"TGATGTCACCGTCTGTCAATGAATATTATAGAAGGTATGAAGGTGTAATTACCATAATAACAAAAC" \
"ACCCTGTCTTTAGGGCTGACCTTTCGTCCTTTGACCTCCTCAGCCTCCATTCCCATCTTCGCTCAG" \
"ACTGCAAGTATGTTTGTATTAATGTACTATGTAGGCGGCTTGGAGCTGGGGAACATTCTTTCATTC" \
"TAAGAATTTGCAGATGCTGACGTTCCTCCTTTCTGCCCCTACAGGCTCTGGCTTATCCAAGAGGCA" \
"AACACTGACCTCTGGTAATTAAAATCCTAGTTCTTTTCTTTTGTCTTTTCCAGGAATTTGACAAGA" \
"AGTACAATCCCACCTGGCATTGCATCGTGGGGAGGAACTTCGGTAGTTATGTGACACATGAAACCA" \
"AACACTTCATCTACTTCTACCTGGGCCAAGTGGCCATTCTTCTGTTCAAATCTGGTTAAAAGCATG" \
"GACTGTGCCACACACCCAGTGATCCATCCAAAAACAAGGACTGCAGCCTAAATTCCAAATACCAGA" \
"GACTGAAATTTTCAGCCTTGCTAAGGGAACATCTCGATGTTTGAACCTTTGTTGTGTTTTGTACAG" \
"GGCATTCTCTGTACTAGTTTGTCGTGGTTATAAAACAATTAGCAGAATAGCCTACATTTGTATTTA" \
"TTTTCTATTCCATACTTCTGCCCACGTTGTTTTCTCTCAAAATCCATTCCTTTAAAAAATAAATCT" \
"GATGCAGATGTGTATGTGTGTG"
expected.add_cds_sequence(cds)
expected.add_genomic_sequence(genomic, offset=10)
return expected
