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from nose.tools import eq_, with_setup
from .data import (
custom_mouse_genome_grcm38_subset,
setup_init_custom_mouse_genome
)
@with_setup(setup=setup_init_custom_mouse_genome)
def test_mouse_ENSMUSG00000017167():
"""
GTF cropped from ftp://ftp.ensembl.org/pub/release-81/gtf/mus_musculus/
Mus_musculus.GRCm38.81.gtf.gz via:
grep "ENSMUSG00000017167" Mus_musculus.GRCm38.81.gtf
Transcript FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/
fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz via:
grep "ENSMUSG00000017167" Mus_musculus.GRCm38.cdna.all.fa -A 50
ncRNA FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/
fasta/mus_musculus/cdna/Mus_musculus.GRCm38.ncrna.fa.gz via:
grep "ENSMUSG00000088969" Mus_musculus.GRCm38.ncrna.fa -A 2
Protein FASTA cropped from ftp://ftp.ensembl.org/pub/release-81/fasta/
mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz via:
grep "ENSMUSG00000017167" Mus_musculus.GRCm38.pep.all.fa -A 50
Tested against:
http://useast.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000017167
"""
genes_cntnap1 = custom_mouse_genome_grcm38_subset.genes_by_name("Cntnap1")
eq_(len(genes_cntnap1), 1)
gene_cntnap1 = genes_cntnap1[0]
transcripts_cntnap1 = gene_cntnap1.transcripts
eq_(len(transcripts_cntnap1), 2)
transcripts_coding_cntnap1 = [
transcript
for transcript in transcripts_cntnap1
if transcript.biotype == "protein_coding"
]
eq_(len(transcripts_coding_cntnap1), 1)
transcript_cntnap1 = transcripts_coding_cntnap1[0]
eq_(transcript_cntnap1.sequence[:120],
("GAGAGAAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA"
"GAGAGAGAGAGATTGGGGGTAGGAGAGAGGGAAGGGTGGATAAGGACGGAAAAAAGCTTT"))
eq_(transcript_cntnap1.protein_sequence[:120],
("MMSLRLFSILLATVVSGAWGWGYYGCNEELVGPLYARSLGASSYYGLFTTARFARLHGIS"
"GWSPRIGDPNPWLQIDLMKKHRIRAVATQGAFNSWDWVTRYMLLYGDRVDSWTPFYQKGH"))
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