def genome():
data = GFGenome(
reference_name='hg38_test',
annotation_name='hg38_chr22_test',
gtf_path_or_url="./tests/data/gencode.v24.annotation_chr22.gtf",
transcript_fasta_paths_or_urls="./tests/data/hg38_chr22.fa",
)
return data
def gene():
data1 = GFGenome(
reference_name='hg38_test',
annotation_name='hg38_chr22_test',
gtf_path_or_url="./tests/data/gencode.v24.annotation_chr22.gtf",
transcript_fasta_paths_or_urls="./tests/data/hg38_chr22.fa",
)
test_gene = GFGene('ENSG00000008735.13', 'MAPK8IP2', '22', 50600685,
50613981, '+', None, data1)
return test_gene
def FivePrimeUTRSeq_object():
data = GFGenome(
reference_name='hg38_test_FivePrimeUTRSeq',
annotation_name='hg38_chr22_test_FivePrimeUTRSeq',
gtf_path_or_url=
"./tests/data/gencode.v24.annotation_chr22_FivePrimeUTRSeq_testing.gtf",
transcript_fasta_paths_or_urls="./tests/data/hg38_chr22.fa",
)
UTR_object = FivePrimeUTRSeq(data, False, 22, "+")
return UTR_object
def FivePrimeUTRSeq_object_minus_strand_no_reverse():
data_minus = GFGenome(
reference_name='hg38_test_FivePrimeUTRSeq_minus',
annotation_name='hg38_chr22_test_FivePrimeUTRSeq_minus',
gtf_path_or_url=
"./tests/data/gencode.v24.annotation_chr22_FivePrimeUTRSeq_testing_minus-strand.gtf",
transcript_fasta_paths_or_urls="./tests/data/hg38_chr22.fa",
)
UTR_object = FivePrimeUTRSeq(data_minus, False, 22, "-")
return UTR_object
def transcript2():
data = GFGenome(
reference_name='hg38_test',
annotation_name='hg38_chr22_test',
gtf_path_or_url="./tests/data/gencode.v24.annotation_chr22.gtf",
transcript_fasta_paths_or_urls="./tests/data/hg38_chr22.fa",
)
test_transcript = GFTranscript('ENST00000343518.10', 'POTEH-001', '22',
15690026, 15721522, '+', 'None',
'ENSG00000198062.14', data)
return test_transcript
def transcript():
data = GFGenome(
reference_name='hg38_test',
annotation_name='hg38_chr22_test',
gtf_path_or_url="./tests/data/gencode.v24.annotation_chr22.gtf",
transcript_fasta_paths_or_urls="./tests/data/hg38_chr22.fa",
)
test_transcript = GFTranscript('ENST00000624155.1', 'BAGE5-201', '22',
11066501, 11068089, '-', 'None',
'ENSG00000279973.1', data)
return test_transcript