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import os
from pyensembl import Locus, Genome
def data_path(name):
"""
Return the absolute path to a file in the test/data directory.
The name specified should be relative to test/data.
"""
return os.path.join(os.path.dirname(__file__), "data", name)
# mapping of ensembl releases to transcript IDs for FOXP3-001
FOXP3_001_transcript_id = "ENST00000376207"
TP53_gene_id = "ENSG00000141510"
# beta-catenin interacting protein from the negative strand of chromosome 1
# URL: http://useast.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?
# db=core;g=ENSG00000178585;r=1:9848276-9910336;t=ENST00000377256
CTNNBIP1_004_transcript_id = "ENST00000377256"
# coding sequence for beta-catenin interacting protein (CTNNBIP1-004)
CTNNBIP1_004_CDS = "".join([
"ATG",
"AACCGCGAGGGAGCTCCCGGGAAGAGTCCGGAG",
"GAGATGTACATTCAGCAGAAGGTCCGAGTGCTGCTCATGCTGCGGAAGATGGGATCAAAC",
"CTGACAGCCAGCGAGGAGGAGTTCCTGCGCACCTATGCAGGGGTGGTCAACAGCCAGCTC",
"AGCCAGCTGCCTCCGCACTCCATCGACCAGG",
"GTGCAGAGGACGTGGTGATGGCGTTTTCCAGGTCGGAGACGGAAGACCGGAGGCAG",
"TAG"
])
# 5' UTR for beta-catenin interacting protein (CTNNBIP1-004)
CTNNBIP1_004_UTR5 = "".join([
"TGTGGGTGCAGGTTTCCTGGGCTTGCCAGACACACAGGGCGGCACCTTCCTACTTCTGCC",
"CAGCCACAGCCCTCCCCTCACAGTTGAGCACCTGTTTGCCTGAAGTTAATTTCCAGAAGC",
"AGGAGTCCCCAGAGCCAGGCAGGGGG"])
# 3' UTR for beta-catenin interacting protein (CTNNBIP1-004)
CTNNBIP1_004_UTR3 = \
"CTGCAAAGCCCTTGGAACACCCTGGATGCTGTTGAGGGCCAAGAGATCTGTGTGGCTCC"
CTNNBIP1_004_locus = Locus("1", 9850659, 9878176, "-")
# properties of CTNNBIP1-004's exons copied from
# http://useast.ensembl.org/Homo_sapiens/Transcript/Exons?g=ENSG00000178585;
# r=1:9850659-9878176;redirect=no;t=ENST00000377256
CTTNNIP1_004_exon_ids = [
'ENSE00001473268',
'ENSE00001643659',
'ENSE00001600669',
'ENSE00001267940',
'ENSE00001473265',
]
CTTNNIP1_004_exon_lengths = [
37,
85,
120,
91,
118
]
#
# Information for EGFR from Ensembl website
# Date: March 25th, 2015
# Ensembl Release: 79
#
EGFR_001_name = "EGFR-001"
EGFR_001_transcript_id = "ENST00000275493"
EGFR_001_ccds_id = "CCDS5514"
EGFR_001_protein_id = "ENSP00000275493"
EGFR_001_protein_sequence = "".join([
"MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYV",
"QRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNL",
"QEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQKL",
"TKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVN",
"PEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLS",
"INATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAF",
"ENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKI",
"ISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHP",
"ECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTG",
"PGLEGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPN",
"QALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVD",
"NPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAA",
"RNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTF",
"GSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLV",
"IQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGFFSSPSTSRTPLLSSLSATSNNSTVACI",
"DRNGLQSCPIKEDSFLQRYSSDPTGALTEDSIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPS"
"RDPHYQDPHSTAVGNPEYLNTVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGS"
"TAENAEYLRVAPQSSEFIGA"
])
# 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
MOUSE_ENSMUSG00000017167_PATH = data_path(
"mouse.ensembl.81.partial.ENSMUSG00000017167.gtf")
MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH = data_path(
"mouse.ensembl.81.partial.ENSMUSG00000017167.fa")
MOUSE_ENSMUSG00000088969_NCRNA_FASTA_PATH = data_path(
"mouse.ensembl.81.partial.ncrna.ENSMUSG00000017167.fa")
MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH = data_path(
"mouse.ensembl.81.partial.ENSMUSG00000017167.pep")
custom_mouse_genome_grcm38_subset = Genome(
reference_name="GRCm38",
annotation_name="_test_mouse_ensembl81_subset",
gtf_path_or_url=MOUSE_ENSMUSG00000017167_PATH,
transcript_fasta_paths_or_urls=[MOUSE_ENSMUSG00000017167_TRANSCRIPT_FASTA_PATH],
protein_fasta_paths_or_urls=[MOUSE_ENSMUSG00000017167_PROTEIN_FASTA_PATH])
def setup_init_custom_mouse_genome():
"""
If a unit test needs to start from a cleared cache, add this to the test
setup.
"""
custom_mouse_genome_grcm38_subset.clear_cache()
custom_mouse_genome_grcm38_subset.index()
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