def test_cdna_creation(self):
g = FileBasedGenome(
"Candidatus_carsonella",
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.gtf.gz"
),
None,
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
),
)
g.download_genome()
g.job_transcripts()
ppg.run_pipegraph()
assert g.find_file("genome.fasta").exists()
assert g.find_file("genome.fasta").with_suffix(".fasta.fai").exists()
tf = g.df_transcripts
assert "BAF35033" in tf.index
assert tf.loc["BAF35033"].exons == ((1313, 2816), )
should = dict(
iter_fasta(
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
)))
should = {k[:k.find(b" ")]: v for (k, v) in should.items()}
actual = dict(iter_fasta(g.find_file("cdna.fasta")))
if actual != should:
assert not set(should.keys()).difference(set(actual.keys(
))) # they are all here, we just have more (tRNA...)
for k in should:
assert actual[k] == should[k]
def test_multiple_fasta_files(self, new_pipegraph):
import tempfile
tf = tempfile.NamedTemporaryFile(suffix=".fasta")
tf.write(b">Extra\nAGTC")
tf.flush()
g = FileBasedGenome(
"Candidatus_carsonella",
[
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
tf.name,
],
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.gtf.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
),
)
g.download_genome()
ppg.run_pipegraph()
assert g.get_genome_sequence("Extra", 0, 4) == "AGTC"
assert g.get_chromosome_lengths() == {"Extra": 4, "Chromosome": 159662}
# test that changing the fasta leads to an explosion
new_pipegraph.new_pipegraph()
tf.seek(0, 0)
tf.write(b">Extra\nAGTCA")
tf.flush()
g = FileBasedGenome(
"Candidatus_carsonella",
[
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
tf.name,
],
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.gtf.gz"
),
None,
)
g.download_genome()
with pytest.raises(UpstreamChangedError):
ppg.run_pipegraph()
def test_job_creating_fasta(self, new_pipegraph):
new_pipegraph.quiet = False
def gen_fasta():
import shutil
shutil.copy(
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
"shu.fasta.gz",
)
fasta_job = ppg.FileGeneratingJob("shu.fasta.gz", gen_fasta)
g = FileBasedGenome(
"Candidatus_carsonella",
fasta_job,
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.gtf.gz"
),
None,
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
),
)
g.download_genome()
ppg.run_pipegraph()
assert (
g.get_cdna_sequence("BAF35032") ==
"ATGAATACTATATTTTCAAGAATAACACCATTAGGAAATGGTACGTTATGTGTTATAAGAAT"
"TTCTGGAAAAAATGTAAAATTTTTAATACAAAAAATTGTAAAAAAAAATATAAAAGAAAAAATAG"
"CTACTTTTTCTAAATTATTTTTAGATAAAGAATGTGTAGATTATGCAATGATTATTTTTTTTAAA"
"AAACCAAATACGTTCACTGGAGAAGATATAATCGAATTTCATATTCACAATAATGAAACTATTGT"
"AAAAAAAATAATTAATTATTTATTATTAAATAAAGCAAGATTTGCAAAAGCTGGCGAATTTTTAG"
"AAAGACGATATTTAAATGGAAAAATTTCTTTAATAGAATGCGAATTAATAAATAATAAAATTTTA"
"TATGATAATGAAAATATGTTTCAATTAACAAAAAATTCTGAAAAAAAAATATTTTTATGTATAAT"
"TAAAAATTTAAAATTTAAAATAAATTCTTTAATAATTTGTATTGAAATCGCAAATTTTAATTTTA"
"GTTTTTTTTTTTTTAATGATTTTTTATTTATAAAATATACATTTAAAAAACTATTAAAACTTTTA"
"AAAATATTAATTGATAAAATAACTGTTATAAATTATTTAAAAAAGAATTTCACAATAATGATATT"
"AGGTAGAAGAAATGTAGGAAAGTCTACTTTATTTAATAAAATATGTGCACAATATGACTCGATTG"
"TAACTAATATTCCTGGTACTACAAAAAATATTATATCAAAAAAAATAAAAATTTTATCTAAAAAA"
"ATAAAAATGATGGATACAGCAGGATTAAAAATTAGAACTAAAAATTTAATTGAAAAAATTGGAAT"
"TATTAAAAATATAAATAAAATTTATCAAGGAAATTTAATTTTGTATATGATTGATAAATTTAATA"
"TTAAAAATATATTTTTTAACATTCCAATAGATTTTATTGATAAAATTAAATTAAATGAATTAATA"
"ATTTTAGTTAACAAATCAGATATTTTAGGAAAAGAAGAAGGAGTTTTTAAAATAAAAAATATATT"
"AATAATTTTAATTTCTTCTAAAAATGGAACTTTTATAAAAAATTTAAAATGTTTTATTAATAAAA"
"TCGTTGATAATAAAGATTTTTCTAAAAATAATTATTCTGATGTTAAAATTCTATTTAATAAATTT"
"TCTTTTTTTTATAAAGAATTTTCATGTAACTATGATTTAGTGTTATCAAAATTAATTGATTTTCA"
"AAAAAATATATTTAAATTAACAGGAAATTTTACTAATAAAAAAATAATAAATTCTTGTTTTAGAA"
"ATTTTTGTATTGGTAAATGA")
def test_transcript_wrong_order(self):
g = FileBasedGenome(
"Candidatus_carsonella",
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.transcript_wrong_order.gtf.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
),
)
job = g.job_transcripts()
with pytest.raises(ppg.RuntimeError):
ppg.run_pipegraph()
assert "start > stop" in str(job.exception)
def test_transcript_transcript_outside_gene(self):
g = FileBasedGenome(
"Candidatus_carsonella",
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.transcript_outside_gene.gtf.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
),
)
job = g.job_transcripts()
with pytest.raises(ppg.RuntimeError):
ppg.run_pipegraph()
assert "Transcript outside of gene" in str(job.exception)
assert isinstance(job.exception, ValueError)
def test_transcripts_unique_check(self):
g = FileBasedGenome(
"Candidatus_carsonella",
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.gtf.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
),
)
g.get_additional_gene_gtfs = lambda: [
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.more_transcripts.gtf.gz"
)
]
g.download_genome()
job = g.job_transcripts()
with pytest.raises(ppg.RuntimeError):
ppg.run_pipegraph()
assert "transcript_stable_ids were not unique" in str(job.exception)
def test_get_gtf_using_additional_gtf(self):
g = FileBasedGenome(
"Candidatus_carsonella",
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.gtf.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
),
)
g.get_additional_gene_gtfs = lambda: [
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.additional.gtf.gz"
)
]
g.download_genome()
j = g.job_genes()
for x in j.prerequisites:
if hasattr(x, "filenames"):
print(x, x.filenames)
if (get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.additional.gtf.gz"
)) in x.filenames:
break
else:
assert False # wrong preqs
ppg.run_pipegraph()
assert "TEST1_001" in g.df_genes.index
def test_protein_creation(self):
g = FileBasedGenome(
"Candidatus_carsonella",
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.gtf.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
),
None,
ProkaryoticCode(),
)
g.download_genome()
g.job_transcripts()
ppg.run_pipegraph()
should = dict(
iter_fasta(
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
)))
should = {k[:k.find(b" ")]: v for (k, v) in should.items()}
actual = dict(iter_fasta(g.find_file("pep.fasta")))
if actual != should:
assert not set(should.keys()).difference(set(actual.keys(
))) # they are all here, we just have more (tRNA...)
for k in should:
if actual[k] != should[k]:
print(k)
print(len(actual[k]))
print(len(should[k]))
print(actual[k])
print(should[k])
# print(g.get_cds_sequence(k.decode('utf-8')))
# else:
# print('ok', k)
# assert actual[k] == should[k]
assert False
def get_Candidatus_carsonella_ruddii_pv(name=None, **kwargs):
"""A FilebasedGenome used by other libraries for their tests"""
from mbf_genomes import FileBasedGenome
if name is None: # pragma: no cover
name = "Candidatus_carsonella"
return FileBasedGenome(
name,
get_sample_path(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
get_sample_path(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.gtf.gz"
),
get_sample_path(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
),
get_sample_path(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
),
**kwargs,
)
def test_indexing(self):
g = FileBasedGenome(
"Candidatus_carsonella",
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.42.gtf.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
),
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.pep.all.fa.gz"
),
)
g.download_genome()
g.job_transcripts()
g.job_genes()
with pytest.raises(ValueError):
g.df_transcripts
with pytest.raises(ValueError):
g.df_genes
ppg.run_pipegraph()
assert g.find_file("genome.fasta").exists()
assert g.find_prebuild("genome.fasta") == g.genome_fasta_dependencies
assert g.find_file("genome.fasta").with_suffix(".fasta.fai").exists()
for should_file, actual_file in [
(
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
g.find_file("genome.fasta"),
),
(
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.cdna.all.fa.gz"
),
g.find_file("cdna.fasta"),
),
]:
should = dict(iter_fasta(should_file))
should = {k[:k.find(b" ")]: v for (k, v) in should.items()}
actual = dict(iter_fasta(actual_file))
if should != actual:
assert len(should) == len(actual)
assert set(should.keys()) == set(actual.keys())
assert False == should_file # noqa:E712
tf = g.df_transcripts
assert "BAF35033" in tf.index
assert not hasattr(g, "_transcripts")
assert tf.loc["BAF35033"].exons == ((1313, 2816), )
gf = g.df_genes
assert len(gf) == 246
# transcript_stable_ids is tuples, this genome has only one transcript
# per gene
assert set([len(x) for x in gf.transcript_stable_ids]) == set([1])
assert g.find_file("pep.fasta").exists()
assert g.find_prebuild("pep.fasta") == g.protein_fasta_dependencies
assert g.find_file("pep.fasta").with_suffix(".fasta.fai").exists()
assert (
g.get_protein_sequence("BAF35037") ==
"MFKFINRFLNLKKRYFYIFLINFFYFFNKCNFIKKKKIYKKIITKKFENYLLKLIIQKYAK")
def test_empty_gtf_and_cdna_and_protein(self):
g = FileBasedGenome(
"Candidatus_carsonella",
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
None,
None,
)
g.download_genome()
assert g.gtf_filename is None
assert g.cdna_fasta_filename is None
g.job_transcripts()
g.job_genes()
g.job_proteins()
ppg.run_pipegraph()
assert len(g.df_transcripts) == 0
assert len(g.get_gtf()) == 0
assert len(g.df_genes) == 0
assert len(g.df_proteins) == 0