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from pyensembl import Locus, Gene, ensembl_grch37, Transcript, Exon
from .common import eq_
def test_Locus_string_representation():
locus = Locus("X", 1000, 1010, "+")
string_repr = str(locus)
expected = "Locus(contig='X', start=1000, end=1010, strand='+')"
eq_(string_repr, expected)
def test_Gene_string_representation():
gene = Gene(
gene_id="ENSG0001",
gene_name="CAPITALISM",
biotype="protein_coding",
contig="Y",
start=1,
end=5,
strand="+",
genome=ensembl_grch37,
)
string_repr = str(gene)
expected = (
"Gene(gene_id='ENSG0001',"
" gene_name='CAPITALISM',"
" biotype='protein_coding',"
" contig='Y',"
" start=1, end=5, strand='+', genome='GRCh37')"
)
eq_(string_repr, expected)
def test_Transcript_string_representation():
transcript = Transcript(
transcript_id="ENST0001",
transcript_name="CAPITALISM-001",
gene_id="ENSG0001",
biotype="protein_coding",
contig="Y",
start=1,
end=5,
strand="+",
genome=ensembl_grch37,
)
expected = (
"Transcript(transcript_id='ENST0001',"
" transcript_name='CAPITALISM-001',"
" gene_id='ENSG0001',"
" biotype='protein_coding',"
" contig='Y',"
" start=1,"
" end=5, strand='+', genome='GRCh37')"
)
string_repr = str(transcript)
eq_(string_repr, expected)
def test_Exon_string_representation():
exon = Exon(
exon_id="ENSE0001",
gene_id="ENSG0001",
gene_name="CAPITALISM",
contig="Y",
start=1,
end=5,
strand="+",
)
expected = (
"Exon(exon_id='ENSE0001',"
" gene_id='ENSG0001',"
" gene_name='CAPITALISM',"
" contig='Y',"
" start=1,"
" end=5, strand='+')"
)
string_repr = str(exon)
eq_(string_repr, expected)
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