def test_get_true_chromosomes(self, mock_download, shared_prebuild):
# we need something with contigs and chromosomes
g = EnsemblGenome("Ustilago_maydis", 33, shared_prebuild)
ppg.run_pipegraph()
should = [
"1",
"2",
"3",
"4",
"5",
"6",
"7",
"8",
"9",
"10",
"11",
"12",
"13",
"14",
"15",
"16",
"17",
"18",
"19",
"20",
"21",
"22",
"23",
"U37796.1", # it is a true chromosome if there's chromosome: in the fasta description
]
all_contigs = should + [
"um_scaf_contig_1.256",
"um_scaf_contig_1.265",
"um_scaf_contig_1.271",
"um_scaf_contig_1.264",
]
assert set(g.get_true_chromosomes()) == set(should)
assert set(g.get_chromosome_lengths()) == set(should + all_contigs)
def test_get_true_chromosomes_genome_without_chromosomes(
self, mock_download, shared_prebuild):
# we need something with contigs and chromosomes
g = EnsemblGenome("Giardia_lamblia", 43, shared_prebuild)
ppg.run_pipegraph()
should = [
"ctg02_1",
"ctg02_2",
"ctg02_3",
"ctg02_4",
"ctg02_5",
"ctg02_6",
"ctg02_7",
"ctg02_8",
"ctg02_9",
"ctg02_10",
"ctg02_11",
"ctg02_12",
"ctg02_13",
"ctg02_14",
"ctg02_15",
"ctg02_16",
"ctg02_17",
"ctg02_18",
"ctg02_19",
"ctg02_20",
"ctg02_21",
"ctg02_22",
"ctg02_23",
"ctg02_24",
"ctg02_25",
"ctg02_26",
"ctg02_27",
"ctg02_28",
"ctg02_29",
"ctg02_30",
"ctg02_31",
"ctg02_32",
"ctg02_33",
"ctg02_34",
"ctg02_35",
"ctg02_36",
"ctg02_37",
"ctg02_38",
"ctg02_39",
"ctg02_40",
"ctg02_41",
"ctg02_42",
"ctg02_43",
"ctg02_44",
"ctg02_45",
"ctg02_46",
"ctg02_47",
"ctg02_48",
"ctg02_49",
"ctg02_50",
"ctg02_51",
"ctg02_52",
"ctg02_53",
"ctg02_54",
"ctg02_55",
"ctg02_56",
"ctg02_57",
"ctg02_58",
"ctg02_59",
"ctg02_60",
"ctg02_61",
"ctg02_62",
"ctg02_63",
"ctg02_64",
"ctg02_65",
"ctg02_66",
"ctg02_67",
"ctg02_68",
"ctg02_69",
"ctg02_70",
"ctg02_71",
"ctg02_72",
"ctg02_73",
"ctg02_74",
"ctg02_75",
"ctg02_76",
"ctg02_77",
"ctg02_78",
"ctg02_79",
"ctg02_80",
"ctg02_81",
"ctg02_82",
"ctg02_83",
"ctg02_84",
"ctg02_85",
"ctg02_86",
"ctg02_87",
"ctg02_88",
"ctg02_89",
"ctg02_90",
"ctg02_91",
"ctg02_92",
"ctg02_93",
"ctg02_94",
"ctg02_95",
"ctg02_96",
"ctg02_97",
"ctg02_99",
"ctg02_98",
"ctg02_100",
"ctg02_101",
"ctg02_102",
"ctg02_103",
"ctg02_104",
"ctg02_105",
"ctg02_106",
"ctg02_107",
"ctg02_108",
"ctg02_109",
"ctg02_110",
"ctg02_111",
"ctg02_112",
"ctg02_113",
"ctg02_114",
"ctg02_115",
"ctg02_116",
"ctg02_117",
"ctg02_118",
"ctg02_120",
"ctg02_119",
"ctg02_121",
"ctg02_122",
"ctg02_123",
"ctg02_124",
"ctg02_125",
"ctg02_127",
"ctg02_126",
"ctg02_129",
"ctg02_128",
"ctg02_130",
"ctg02_131",
"ctg02_132",
"ctg02_133",
"ctg02_134",
"ctg02_135",
"ctg02_136",
"ctg02_137",
"ctg02_138",
"ctg02_139",
"ctg02_140",
"ctg02_141",
"ctg02_142",
"ctg02_144",
"ctg02_143",
"ctg02_145",
"ctg02_146",
"ctg02_147",
"ctg02_148",
"ctg02_149",
"ctg02_151",
"ctg02_150",
"ctg02_152",
"ctg02_153",
"ctg02_155",
"ctg02_154",
"ctg02_157",
"ctg02_156",
"ctg02_158",
"ctg02_159",
"ctg02_160",
"ctg02_161",
"ctg02_162",
"ctg02_163",
"ctg02_164",
"ctg02_165",
"ctg02_167",
"ctg02_168",
"ctg02_166",
"ctg02_169",
"ctg02_170",
"ctg02_171",
"ctg02_172",
"ctg02_174",
"ctg02_176",
"ctg02_175",
"ctg02_178",
"ctg02_177",
"ctg02_179",
"ctg02_180",
"ctg02_181",
"ctg02_183",
"ctg02_182",
"ctg02_184",
"ctg02_185",
"ctg02_186",
"ctg02_187",
"ctg02_188",
"ctg02_189",
"ctg02_190",
"ctg02_191",
"ctg02_193",
"ctg02_192",
"ctg02_194",
"ctg02_196",
"ctg02_195",
"ctg02_197",
"ctg02_198",
"ctg02_200",
"ctg02_199",
"ctg02_201",
"ctg02_202",
"ctg02_203",
"ctg02_204",
"ctg02_206",
"ctg02_208",
"ctg02_207",
"ctg02_205",
"ctg02_209",
"ctg02_210",
"ctg02_211",
"ctg02_212",
"ctg02_214",
"ctg02_213",
"ctg02_215",
"ctg02_216",
"ctg02_220",
"ctg02_218",
"ctg02_221",
"ctg02_217",
"ctg02_219",
"ctg02_223",
"ctg02_222",
"ctg02_224",
"ctg02_225",
"ctg02_226",
"ctg02_227",
"ctg02_228",
"ctg02_229",
"ctg02_231",
"ctg02_230",
"ctg02_232",
"ctg02_234",
"ctg02_235",
"ctg02_233",
"ctg02_237",
"ctg02_238",
"ctg02_236",
"ctg02_239",
"ctg02_241",
"ctg02_240",
"ctg02_242",
"ctg02_245",
"ctg02_243",
"ctg02_246",
"ctg02_244",
"ctg02_247",
"ctg02_249",
"ctg02_250",
"ctg02_248",
"ctg02_252",
"ctg02_251",
"ctg02_253",
"ctg02_254",
"ctg02_255",
"ctg02_256",
"ctg02_257",
"ctg02_258",
"ctg02_259",
"ctg02_260",
"ctg02_173",
"ctg02_261",
"ctg02_262",
"ctg02_263",
"ctg02_266",
"ctg02_265",
"ctg02_268",
"ctg02_264",
"ctg02_267",
"ctg02_269",
"ctg02_271",
"ctg02_270",
"ctg02_273",
"ctg02_272",
"ctg02_274",
"ctg02_275",
"ctg02_276",
"ctg02_277",
"ctg02_278",
"ctg02_279",
"ctg02_280",
"ctg02_282",
"ctg02_281",
"ctg02_283",
"ctg02_284",
"ctg02_285",
"ctg02_286",
"ctg02_287",
"ctg02_289",
"ctg02_288",
"ctg02_290",
"ctg02_291",
"ctg02_292",
"ctg02_293",
"ctg02_294",
"ctg02_295",
"ctg02_296",
"ctg02_297",
"ctg02_298",
"ctg02_299",
"ctg02_300",
"ctg02_301",
"ctg02_302",
"ctg02_303",
"ctg02_304",
"ctg02_305",
"ctg02_306",
]
assert set(g.get_true_chromosomes()) == set(should)
assert set(g.get_true_chromosomes()) == set(g.get_chromosome_lengths())
def test_download(self, new_pipegraph, mock_download, shared_prebuild):
species = "Ashbya_gossypii" # the smallest eukaryotic species at the time of writing this at 2.8 mb
g = EnsemblGenome(species, "41", prebuild_manager=shared_prebuild)
def shorten_genome_fasta(output_path):
with open(g.find_file("genome.fasta")) as op:
head = op.read(1024 * 100)
(output_path / "test.fasta").write_text(head)
test_fasta_job = g.prebuild_manager.prebuild(
f"ensembl/{g.species}_{g.revision}/test_fasta",
"1",
[],
["test.fasta"],
shorten_genome_fasta,
)
test_fasta_job.depends_on(g.download_genome())
g._prebuilds.append(test_fasta_job)
subread = Subread(version="1.6.3")
index = g.build_index(subread, "test.fasta")
subread_old = Subread(version="1.4.3-p1")
index_old = g.build_index(subread_old, "test.fasta")
new_pipegraph.run()
# note that these are not the checksums from CHECKSUMS files (those are fore
# the gziped variants, we keep them ungziped and let the filesystem handle
# the gzip, since we can't rely on the downstream reading gzip...
assert (checksum_file(
g.find_file("genome.fasta")) == "584a734589964a654c7c1dc23b0167ab")
assert (checksum_file(
g.find_file("cdna.fasta")) == "3fc1f19ab829573169cb2488abe39211")
assert (checksum_file(
g.find_file("genes.gtf")) == "8bdeec9b3db5278668dbff8b34e9d93b")
assert (checksum_file(
g.find_file("genes.gtf")) == "8bdeec9b3db5278668dbff8b34e9d93b")
assert (checksum_file(
g.find_file("pep.fasta")) == "9580fd44832d419c38469d657f6e2484")
with pytest.raises(OSError):
g.find_file("no such file")
assert index.name_file("subread_index.reads").exists()
assert index.name_file("subread_index.files").exists()
assert index.name_file("subread_index.00.b.array").exists()
assert index_old.name_file("subread_index.reads").exists()
assert index_old.name_file("subread_index.files").exists()
assert index_old.name_file("subread_index.00.b.array").exists()
assert index.name_file("subread_index.reads") != index_old.name_file(
"subread_index.reads")
assert g.find_file("test.fasta.md5sum").exists()
with pytest.raises(OSError):
assert g.find_file("test.fasta.md5sum.nosuchfile").exists()
assert g.find_prebuild("test.fasta") is test_fasta_job
with pytest.raises(OSError):
assert g.find_prebuild("test.fasta.md5sum.nosuchfile").exists()
assert g.find_file("genome.fasta.fai").exists()
assert g.find_file("cdna.fasta.fai").exists()
new_pipegraph.new_pipegraph()
pb = PrebuildManager(shared_prebuild.prebuilt_path)
g = EnsemblGenome(species, "41", prebuild_manager=pb)
test_fasta_job = g.prebuild_manager.prebuild(
f"ensembl/{g.species}_{g.revision}/test_fasta",
"1",
[],
["test.fasta"],
shorten_genome_fasta,
)
g._prebuilds.append(test_fasta_job)
subread_intermediate = Subread(version="1.5.0")
index_intermediate = g.build_index(subread_intermediate, "test.fasta")
assert index_intermediate.name_file(
"subread_index.reads") == index_old.name_file(
"subread_index.reads")
index_genome = g.build_index(subread_intermediate)
assert "/genome/" in str(index_genome.filenames[0])
assert g.get_chromosome_lengths() == {
"IV": 1_467_287,
"MT": 23564,
"V": 1_519_140,
"III": 907_494,
"II": 870_771,
"VII": 1_800_949,
"I": 693_414,
"VI": 1_836_693,
}
assert g.get_genome_sequence("VI", 20, 30) == "ACCGCTGAGA"
assert (g.get_cdna_sequence("EFAGOT00000000349") ==
"GCTCGCGTGGCGTAATGGCAACGCGTCTGACTTCTAATCAGAAGATTGTGGGTTCGACCC"
"CCACCGTGAGTG")
assert (g.get_protein_sequence("AAS53315") ==
"MFSTRICSLLARPFMVPIVPRFGSALLQKPLNGVVVPQFTRGFKVRTSVKKFCAHCYIVR"
"RKGRVYVYCKSNNKHKQRQG")
assert (g.genetic_code.translate_dna(g.get_cds_sequence("AAS53315")) ==
"MFSTRICSLLARPFMVPIVPRFGSALLQKPLNGVVVPQFTRGFKVRTSVKKFCAHCYIVR"
"RKGRVYVYCKSNNKHKQRQG")
assert (g.genetic_code.translate_dna(
g.get_cds_sequence("AAS53315", g.df_proteins.loc["AAS53315"])) ==
"MFSTRICSLLARPFMVPIVPRFGSALLQKPLNGVVVPQFTRGFKVRTSVKKFCAHCYIVR"
"RKGRVYVYCKSNNKHKQRQG")
with pytest.raises(ValueError):
g.get_cds_sequence("AAS53315", g.df_proteins.loc["AAS53316"])
assert (
g.df_genes_meta.loc["AGOS_ADL186C"]["description"] ==
"Restriction of telomere capping protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q75AV6]"
)