def test_ucsc_refseq():
"""
Testing with a small RefSeq GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
genome = Genome("GRCh38", gtf_path_or_url=UCSC_REFSEQ_PATH)
genome.install()
eq_(len(genome.genes()), 2)
eq_(len(genome.transcripts()), 2)
genes_at_locus = genome.genes_at_locus(1, 67092176)
eq_(len(genes_at_locus), 2)
ids = set([gene.id for gene in genes_at_locus])
eq_(set(["NM_001276352", "NR_075077"]), ids)
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
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
"""
genome = Genome(
reference_name="GRCm38",
gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH,
transcript_fasta_path_or_url=MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH,
protein_fasta_path_or_url=MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH,
)
genome.install()
genes_cntnap1 = genome.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"
),
)
def test_ucsc_gencode():
"""
Testing with a small GENCODE GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
genome = Genome("GRCh38", gtf_path_or_url=UCSC_GENCODE_PATH)
genome.install()
eq_(len(genome.genes()), 7)
eq_(len(genome.transcripts()), 7)
gene_uc001aak4 = genome.gene_by_id("uc001aak.4")
eq_(gene_uc001aak4.id, "uc001aak.4")
eq_(gene_uc001aak4.name, None)
eq_(gene_uc001aak4.biotype, None)
gene_1_17369 = genome.genes_at_locus(1, 17369)
eq_(gene_1_17369[0].id, "uc031tla.1")
transcript_1_30564 = genome.transcripts_at_locus(1, 30564)
eq_(transcript_1_30564[0].id, "uc057aty.1")
