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_pairing_invalid_value(self):
with pytest.raises(ValueError):
Sample(
"Sample_a",
get_sample_data(Path("mbf_align/sample_a")),
False,
pairing="do_what_you_want",
)
with pytest.raises(ValueError):
Sample(
"Sample_a",
get_sample_data(Path("mbf_align/sample_a")),
False,
pairing=False,
)
with pytest.raises(ValueError):
Sample(
"Sample_a",
get_sample_data(Path("mbf_align/sample_a")),
False,
pairing=None,
)
with pytest.raises(ValueError):
Sample(
"Sample_a",
get_sample_data(Path("mbf_align/sample_a")),
False,
pairing=[5],
)
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_lane_paired_only_second(self):
lane = Sample(
"Sample_a",
get_sample_data(Path("mbf_align/sample_b")),
False,
vid="VA000",
pairing="only_second",
)
assert lane.vid == "VA000"
temp_job = lane.prepare_input()
real_job = lane.save_input()
ppg.run_pipegraph()
assert not Path(temp_job.filenames[0]).exists()
assert len(temp_job.filenames) == 1
assert Path(real_job.filenames[0]).exists()
assert len(real_job.filenames) == 1
assert not "_R1_" in real_job.filenames[0]
assert ".fastq.gz" in real_job.filenames[0]
should = b""
for input_fn in [
(get_sample_data(Path("mbf_align/sample_b") / "a_R2_.fastq.gz"))
]:
with gzip.GzipFile(input_fn, "r") as op:
should += op.read()
with gzip.GzipFile(real_job.filenames[0], "r") as op:
actual = op.read()
assert actual == should
def test_lane_paired_filtered(self):
lane = Sample(
"Sample_a",
get_sample_data(Path("mbf_align/sample_b")),
False,
vid="VA000",
pairing="paired",
fastq_processor=fastq2.Paired_Filtered(lambda *args: True),
)
assert lane.vid == "VA000"
temp_job = lane.prepare_input()
real_job = lane.save_input()
ppg.run_pipegraph()
assert not Path(temp_job.filenames[0]).exists()
assert not Path(temp_job.filenames[1]).exists()
assert Path(real_job.filenames[0]).exists()
assert Path(real_job.filenames[1]).exists()
assert "_R1_" in real_job.filenames[0]
assert "_R2_" in real_job.filenames[1]
assert ".fastq.gz" in real_job.filenames[0]
assert ".fastq.gz" in real_job.filenames[1]
for input_fn, output_fn in zip(
[
(get_sample_data(Path("mbf_align/sample_b") / "a_R1_.fastq.gz")),
(get_sample_data(Path("mbf_align/sample_b") / "a_R2_.fastq.gz")),
],
real_job.filenames,
):
with gzip.GzipFile(output_fn, "r") as op:
actual = op.read()
with gzip.GzipFile(input_fn, "r") as op:
should = op.read()
assert actual == should
def test_FASTQsFromPrefix():
fn1 = Path(get_sample_data(Path("mbf_align/sample_d") / "a_R1_.fastq.gz"))
fn2 = Path(get_sample_data(Path("mbf_align/sample_d") / "a_R2_.fastq.gz"))
fn_prefix = Path(get_sample_data(Path("mbf_align/sample_d") / "a"))
o = FASTQsFromPrefix(fn_prefix)
str(o)
assert o() == [(fn1.resolve(), fn2.resolve())]
def test_subtraction_by_read(self):
from mbf_sampledata import get_human_22_fake_genome
genome = get_human_22_fake_genome()
lane = mbf_align.AlignedSample(
"test_lane",
get_sample_data(Path("mbf_align/rnaseq_spliced_chr22.bam")),
genome,
False,
"AA123",
) # index creation is automatic
lane2 = mbf_align.AlignedSample(
"test_lane2",
get_sample_data(Path("mbf_align/rnaseq_spliced_chr22.bam")),
genome,
False,
"AA124",
) # index creation is automatic
lane3 = mbf_align.AlignedSample(
"test_lane3",
get_sample_data(Path("mbf_align/chipseq_chr22.bam")),
genome,
False,
"AA123",
) # index creation is automatic
lane3_subset = mbf_align.AlignedSample(
"test_lane3_subset",
get_sample_data(Path("mbf_align/chipseq_chr22_subset.bam")),
genome,
False,
"AA123",
) # index creation is automatic
lane_empty = lane.post_process(
mbf_align.post_process.SubtractOtherLane(lane2), new_name="empty")
lane_full = lane.post_process(
mbf_align.post_process.SubtractOtherLane(lane3), new_name="full")
lane_some = lane3.post_process(
mbf_align.post_process.SubtractOtherLane(lane3_subset),
result_dir="results/aligned/shu",
)
qc_jobs = [
lane_some.post_processor_qc_jobs, lane_full.post_processor_qc_jobs
]
prune_qc(lambda job: job in qc_jobs)
ppg.run_pipegraph()
assert Path(lane_empty.get_bam_names()[1]).exists()
assert Path(lane_full.get_bam_names()[1]).exists()
assert lane_empty.mapped_reads() == 0
assert lane_full.mapped_reads() == lane.mapped_reads()
assert lane.mapped_reads() != 0
assert (lane_some.mapped_reads() == lane3.mapped_reads() -
lane3_subset.mapped_reads())
assert lane3_subset.mapped_reads(
) # make sure there was something to subtract
assert "shu" in lane_some.get_bam_names()[0]
assert_image_equal(qc_jobs[0].filenames[0], "_result_dir")
assert_image_equal(qc_jobs[0].filenames[0])
def test_FASTQsFromFilesPaired_build_strategy():
fn = Path(get_sample_data(Path("mbf_align/sample_b") / "a_R1_.fastq.gz"))
fn2 = Path(
get_sample_data(
Path("mbf_align/sample_b") / ".." / "sample_b" / "a_R2_.fastq.gz"
)
)
o = build_fastq_strategy([fn, fn2])
assert o() == [(fn.resolve(), fn2.resolve())]
def test_FASTQsFromFilePaired():
fn = Path(get_sample_data(Path("mbf_align/sample_b") / "a_R1_.fastq.gz"))
fn2 = Path(
get_sample_data(
Path("mbf_align/sample_b") / ".." / "sample_b" / "a_R2_.fastq.gz"
)
)
o = FASTQsFromFile(fn, fn2)
assert o() == [(fn.resolve(), fn2.resolve())]
def test_fastqs_join():
fn = Path(get_sample_data(Path("mbf_align/sample_b") / "a_R1_.fastq.gz"))
fn2 = Path(
get_sample_data(
Path("mbf_align/sample_b") / ".." / "sample_b" / "a_R2_.fastq.gz"
)
)
a = FASTQsFromFiles([fn, fn2])
b = FASTQsFromFile(fn)
c = FASTQsFromFile(fn2)
d = FASTQsJoin([a, b, c])
o = d()
assert o == [(fn.resolve(), fn2.resolve()), (fn.resolve(),), (fn2.resolve(),)]
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_filtered_paired(new_pipegraph):
import gzip
r1_name_found = [False]
r1_qual_found = [False]
r2_name_found = [False]
r2_qual_found = [False]
def f(seq1, qual1, name1, seq2, qual2, name2):
if name1 == b"HWI-C00113:209:HJCNTBCX2:2:2206:9418:13942 1:N:0:ATCACG":
r1_name_found[0] = True
if qual1 == b"DDDDDIIIIIIIIIIIIIIIIIIIIII/<FHHIII<<CHHGHHIHHIIIIH":
r1_qual_found[0] = True
if name2 == b"HWI-C00113:209:HJCNTBCX2:2:2206:10802:17968 1:N:0:ATCACG":
r2_name_found[0] = True
if qual2 == b"DDDDDIIIIIIIIIIIIIIII1<FHHI/<GHIIII/<EHIIHII/<DHIID":
r2_qual_found[0] = True
return seq1.startswith(b"G") and seq2.startswith(b"G")
x = fastq2.Paired_Filtered(f)
of1 = "output_R1.fastq"
of2 = "output_R2.fastq"
tf1 = open("input_R1_.fastq", "wb")
tf2 = open("input_R2_.fastq", "wb")
with gzip.GzipFile(
get_sample_data(Path("mbf_align/sample_b") / "a_R1_.fastq.gz"),
"rb") as op_in:
tf1.write(op_in.read())
tf1.flush()
with gzip.GzipFile(
get_sample_data(Path("mbf_align/sample_b") / "a_R2_.fastq.gz"),
"rb") as op_in:
tf2.write(op_in.read())
tf2.flush()
x.generate_aligner_input_paired(of1, of2, [(tf1.name, tf2.name)], False)
assert r1_name_found[0]
assert r2_name_found[0]
assert r1_qual_found[0]
assert r2_qual_found[0]
actual1 = Path(of1).read_text()
actual2 = Path(of2).read_text()
assert actual1.count("\n") == 4
assert "@HWI-C00113:209:HJCNTBCX2:2:2206:9559:13855 1:N:0:ATCACG" in actual1
assert "GCCCAATGTTCGAAATTGCTATTCTACGACAAGGTGCCAGATCTCATCTGA" in actual1
assert actual2.count("\n") == 4
assert "@HWI-C00113:209:HJCNTBCX2:2:2206:11052:17798 1:N:0:ATCACG" in actual2
assert "GTCGGTCCTGAGAGATGGGCGGGCGCCGTTCCGAAAGTACGGGCGATGGCC" in actual2
def test_quality_raises_on_0_return(new_pipegraph):
with pytest.raises(ValueError):
fastq2.QualityFilter(lambda qual, seq: 0).generate_aligner_input(
"test.fastq",
[str(get_sample_data(Path("mbf_align/sample_a/a.fastq")))],
False,
)
def test_from_existing_bam(self):
bam_path = get_sample_data(Path("mbf_align/ex2.bam"))
bam_job = ppg.FileInvariant(bam_path)
genome = object()
lane = mbf_align.AlignedSample("test_lane", bam_job, genome, False,
"AA123")
assert lane.name == "test_lane"
assert lane.load()[0] is bam_job
assert isinstance(lane.load()[1], ppg.FileInvariant)
assert lane.genome is genome
assert not lane.is_paired
assert lane.vid == "AA123"
with pytest.raises(ValueError):
mbf_align.AlignedSample("test_lane", bam_job, genome, False,
"AA123")
lane2 = mbf_align.AlignedSample("test_lane2", bam_job, genome, True,
"AA123")
assert lane2.is_paired
b = lane.get_bam()
assert isinstance(b, pysam.Samfile)
b = lane.get_unique_aligned_bam()
assert isinstance(b, pysam.Samfile)
assert lane.get_bam_names()[0] == bam_path
assert lane.get_bam_names()[1] == bam_path + ".bai"
assert lane.mapped_reads() == 8
assert lane.unmapped_reads() == 0
for job in get_qc_jobs():
assert job._pruned
def test_iter_fasta():
fn = get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
)
a = list(iter_fasta(fn))
assert len(a[0][1]) == 159662
b = list(iter_fasta(fn, block_size=10))
assert a == b
def test_paired_modes(self):
with pytest.raises(PairingError):
lane = Sample(
"Sample_a",
get_sample_data(Path("mbf_align/sample_b")),
False,
vid="VA000",
)
lane.prepare_input()
def gen_fasta():
import shutil
shutil.copy(
get_sample_data(
"mbf_genomes/Candidatus_carsonella_ruddii_pv.ASM1036v1.dna.toplevel.fa.gz"
),
"shu.fasta.gz",
)
def test_FASTQsFromFolder():
folder = Path(get_sample_data(Path("mbf_align/sample_a")))
o = FASTQsFromFolder(folder)
import pprint
pprint.pprint(o())
assert o() == [
((folder / "a.fastq").resolve(),),
((folder / "b.fastq.gz").resolve(),),
]
def test_fastqc(self):
from mbf_qualitycontrol import get_qc_jobs
lane = Sample(
"Sample_a", get_sample_data(Path("mbf_align/sample_a")), False, vid="VA000"
)
qc_jobs = list(get_qc_jobs())
assert len(qc_jobs) == 1
assert "results/lanes/Sample_a/FASTQC/sentinel.txt" in qc_jobs[0].filenames
assert lane.prepare_input() in qc_jobs[0].prerequisites
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 test_lane_paired_missing_R2(self):
lane = Sample(
"Sample_a",
get_sample_data(Path("mbf_align/sample_a")),
False,
vid="VA000",
pairing="paired",
)
with pytest.raises(PairingError):
lane.prepare_input()
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_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_read_creator_must_be_fastq_right_now(new_pipegraph):
with pytest.raises(ValueError):
fastq2.Straight().generate_aligner_input(
"test.fastq",
[str(get_sample_data(Path("mbf_align/sample_a)/a.fastq")))],
False,
"fail",
)
with pytest.raises(ValueError):
fastq2.Filtered(lambda seq, qual, name: True).generate_aligner_input(
"test.fastq",
[str(get_sample_data(Path("mbf_align/sample_a)/a.fastq")))],
False,
"fail",
)
with pytest.raises(ValueError):
fastq2.QualityFilter(lambda qual, seq: True).generate_aligner_input(
"test.fastq",
[str(get_sample_data(Path("mbf_align/sample_a)/a.fastq")))],
False,
"fail",
)
def test_to_fastq(self):
bam_path = get_sample_data(Path("mbf_align/ex2.bam"))
bam_job = ppg.FileInvariant(bam_path)
genome = object()
lane = mbf_align.AlignedSample("test_lane", bam_job, genome, False,
"AA123")
fastq_path = "out.fastq"
lane.to_fastq(fastq_path)
ppg.run_pipegraph()
assert Path(fastq_path).exists()
assert (Path(fastq_path).read_text() == """@read_28833_29006_6945
AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG
+
<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<
@read_28701_28881_323b
TGCAAGGCCGCATCGGCCAAGGCCAAGATATAGGT
+
<<<<7<<<<<<<<<<<<;6<<<:;7<<<<;<<<<<
@read_28701_28881_323c
TGCAAGGCCGCATCGGCCAAGGCCAAGATATAGGT
+
<<<<7<<<<<<<<<<<<;6<<<:;7<<<<;<<<<<
@read_28701_28881_324a
TGCAAGGCCGCATCGGCCAAGGCCAAGATATAGGT
+
<<<<7<<<<<<<<<<<<;6<<<:;7<<<<;<<<<<
@read_28701_28881_324b
TGCAAGGCCGCATCGGCCAAGGCCAAGATATAGGT
+
<<<<7<<<<<<<<<<<<;6<<<:;7<<<<;<<<<<
@read_28701_28881_324c
TGCAAGGCCGCATCGGCCAAGGCCAAGATATAGGT
+
<<<<7<<<<<<<<<<<<;6<<<:;7<<<<;<<<<<
@test_clipped1
AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG
+
<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<
@test_clipped1
AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG
+
<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<
""")
lane2 = mbf_align.AlignedSample("test_lane2",
bam_job,
genome,
is_paired=True,
vid="AA123")
with pytest.raises(ValueError):
lane2.to_fastq(
"nope.fastq") # no support for paired end data at this point
def prep_lane(self):
from mbf_sampledata import get_human_22_fake_genome
# straight from chr22 of the human genome
genome = get_human_22_fake_genome()
lane = mbf_align.AlignedSample(
"test_lane",
get_sample_data(Path("mbf_align/rnaseq_spliced_chr22.bam")),
genome,
False,
"AA123",
)
return lane
def test_lane(self):
lane = Sample(
"Sample_a", get_sample_data(Path("mbf_align/sample_a")), False, vid="VA000"
)
assert lane.vid == "VA000"
temp_job = lane.prepare_input()
real_job = lane.save_input()
ppg.run_pipegraph()
assert not Path(temp_job.filenames[0]).exists()
assert Path(real_job.filenames[0]).exists()
with gzip.GzipFile(real_job.filenames[0], "r") as op:
lines = op.readlines()
assert len(lines) == 20 + 20
def test_missing_index_file(self):
bam_path = get_sample_data(Path("mbf_align/ex2.bam"))
no_index = "noindex.bam"
shutil.copy(bam_path, no_index)
genome = object()
lane = mbf_align.AlignedSample("test_lane", no_index, genome, False,
"AA123")
assert isinstance(lane.load()[0], ppg.FileInvariant)
assert isinstance(lane.load()[1], ppg.FileGeneratingJob)
assert lane.load()[1].job_id != "noindex.bam.bai"
assert lane.load()[0] in lane.load()[1].prerequisites
with pytest.raises(FileNotFoundError):
lane.mapped_reads()
ppg.run_pipegraph()
assert lane.mapped_reads() == 8
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()