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 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
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 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_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___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 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___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 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
