def test_build_and_align_paired_end(self, new_pipegraph, per_run_store):
new_pipegraph.quiet = False
s = Subread()
data_path = Path(__file__).parent / "sample_data"
index_name = Path("subread_index_dir/srf")
build_job = s.build_index_job(data_path / "genome.fasta", None,
index_name)
align_job = s.align_job(
data_path / "sample_R1_.fastq",
data_path / "sample_R2_.fastq",
index_name,
"out/out.bam",
{"input_type": "rna"},
)
align_job.depends_on(build_job)
new_pipegraph.run()
assert (Path("out") / "out.bam").exists()
def test_build_and_align(self, new_pipegraph, per_run_store):
new_pipegraph.quiet = False
s = Subread()
data_path = Path(__file__).parent / "sample_data"
index_name = Path("subread_index_dir/srf")
build_job = s.build_index_job([data_path / "genome.fasta"], None,
index_name)
align_job = s.align_job(
data_path / "sample.fastq",
None,
index_name,
"out/out.bam",
{"input_type": "dna"},
)
align_job.depends_on(build_job)
new_pipegraph.run()
assert (Path("out") / "out.bam").exists()
assert s.get_alignment_stats((Path("out") / "out.bam")) == {
"Uniquely mapped": 1,
"Multi-mapping": 0,
"Unmapped": 0,
}
def test_raises_on_invalid_input_type(self, new_pipegraph, per_run_store):
data_path = Path(__file__).parent / "sample_data"
index_name = Path("subread_index_dir/srf")
s = Subread()
with pytest.raises(ValueError):
s.align_job(data_path / "sample.fastq", None, index_name,
"out/out.bam", {})
with pytest.raises(ValueError):
s.align_job(
data_path / "sample.fastq",
None,
index_name,
"out/out.bam",
{"input_type": "shu"},
)
def test_get_index_version_range(self, new_pipegraph, per_run_store):
s = Subread(version="1.4.3-p1")
assert s.get_index_version_range() == ("0.1", "1.5.99")
s = Subread(version="1.6.3")
assert s.get_index_version_range() == ("1.6", None)
def test_cant_call_subread_run2(self, new_pipegraph, per_run_store):
s = Subread()
s.run("out", ["subread-align", "something"])
with pytest.raises(ValueError):
new_pipegraph.run()
def test_cant_call_subread_run(self, new_pipegraph, per_run_store):
s = Subread()
s.run("out", None)
with pytest.raises(ValueError):
new_pipegraph.run()
def test_subread_older_download(self, new_pipegraph, per_test_store):
s = Subread('1.5.0')
assert s.version == '1.5.0'
s.store.unpack_version(s.name, s.version)
assert s.path.exists()
def test_build_index(self, new_pipegraph, per_run_store):
s = Subread('_latest')
data_path = Path(__file__).parent / "sample_data"
s.build_index([data_path / "genome.fasta"], None, "shu")
assert Path("shu/stdout.txt").exists()
assert Path("shu/subread_index.reads").exists()
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]"
)