def test_empty_input_succeed(self):
inDir = util.file.get_test_input_path()
inBam = os.path.join(inDir, 'empty.bam')
clipDb = os.path.join(inDir, 'clipDb.fasta')
with util.file.tempfname('fasta') as outFasta:
assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, out_fasta=outFasta)
self.assertEqual(os.path.getsize(outFasta), 0)
def test_empty_input_succeed(self):
inDir = util.file.get_test_input_path()
inBam = os.path.join(inDir, 'empty.bam')
clipDb = os.path.join(inDir, 'clipDb.fasta')
with util.file.tempfname('fasta') as outFasta:
assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, out_fasta=outFasta)
self.assertEqual(os.path.getsize(outFasta), 0)
def test_always_succeed(self):
inDir = util.file.get_test_input_path(self)
inBam = os.path.join(inDir, '..', 'almost-empty.bam')
clipDb = os.path.join(inDir, 'clipDb.fasta')
with util.file.tempfname('.fasta') as outFasta:
assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, out_fasta=outFasta, spades_opts='--bad-option',
always_succeed=True)
self.assertEqual(os.path.getsize(outFasta), 0)
def test_always_succeed(self):
inDir = util.file.get_test_input_path(self)
inBam = os.path.join(inDir, '..', 'almost-empty.bam')
clipDb = os.path.join(inDir, 'clipDb.fasta')
with util.file.tempfname('.fasta') as outFasta:
assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, out_fasta=outFasta, spades_opts='--bad-option',
always_succeed=True)
self.assertEqual(os.path.getsize(outFasta), 0)
def test_assembly(self):
inDir = util.file.get_test_input_path(self)
inBam = os.path.join(inDir, '..', 'G5012.3.subset.bam')
clipDb = os.path.join(inDir, 'clipDb.fasta')
with util.file.tempfname('.fasta') as outFasta:
assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, out_fasta=outFasta)
self.assertGreater(os.path.getsize(outFasta), 0)
contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
print('test_assembly_contigs_lens:', contig_lens)
self.assertEqual(contig_lens, [168, 170, 177, 180, 184, 187, 190, 191, 195, 197, 211, 243, 244, 247, 328, 348, 430])
def test_assembly(self):
inDir = util.file.get_test_input_path(self)
inBam = os.path.join(inDir, '..', 'G5012.3.subset.bam')
clipDb = os.path.join(inDir, 'clipDb.fasta')
with util.file.tempfname('.fasta') as outFasta:
assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, min_contig_len=180, out_fasta=outFasta)
self.assertGreater(os.path.getsize(outFasta), 0)
contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
#import sys
#print('test_assembly_contigs_lens:', contig_lens, file=sys.stderr)
self.assertEqual(contig_lens, [180, 184, 187, 190, 191, 194, 197, 211, 243, 244, 247, 288, 328, 348, 430])
def test_assembly(self):
inDir = util.file.get_test_input_path(self)
inBam = os.path.join(inDir, '..', 'G5012.3.subset.bam')
clipDb = os.path.join(inDir, 'clipDb.fasta')
with util.file.tempfname('.fasta') as outFasta:
assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, min_contig_len=180, out_fasta=outFasta)
self.assertGreater(os.path.getsize(outFasta), 0)
contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
#import sys
#print('test_assembly_contigs_lens:', contig_lens, file=sys.stderr)
self.assertEqual(contig_lens, [190, 195, 197, 222, 243, 247, 359])
def test_assembly(self):
inDir = util.file.get_test_input_path(self)
inBam = os.path.join(inDir, '..', 'G5012.3.subset.bam')
with util.file.tempfname('.fasta') as outFasta:
assembly.assemble_spades(inBam=inBam, outFasta=outFasta, threads=4)
self.assertGreater(os.path.getsize(outFasta), 0)
contig_lens = list(
sorted(
len(seq.seq)
for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
self.assertEqual(contig_lens, [
168, 177, 180, 183, 184, 187, 190, 191, 195, 197, 201, 211,
243, 244, 247, 294, 319, 328, 348
])
def test_assembly_with_previously_assembled_contigs(self):
inDir = util.file.get_test_input_path(self)
inBam = os.path.join(inDir, '..', 'G5012.3.subset.bam')
previously_assembled_contigs = os.path.join(inDir,
'trinity_contigs.fasta')
with util.file.tempfname('.fasta') as outFasta:
assembly.assemble_spades(
inBam=inBam,
previously_assembled_contigs=previously_assembled_contigs,
outFasta=outFasta,
threads=1,
mem_limit_gb=1)
self.assertGreater(os.path.getsize(outFasta), 0)
contig_lens = list(
sorted(
len(seq.seq)
for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
self.assertEqual(
contig_lens,
[111, 140, 184, 211, 243, 244, 294, 321, 328, 348, 430])
def test_assembly_with_previously_assembled_contigs(self):
inDir = util.file.get_test_input_path(self)
inBam = os.path.join(inDir, '..', 'G5012.3.subset.bam')
clipDb = os.path.join(inDir, 'clipDb.fasta')
previously_assembled_contigs = os.path.join(inDir,
'trinity_contigs.fasta')
with util.file.tempfname('.fasta') as outFasta:
assembly.assemble_spades(
in_bam=inBam,
clip_db=clipDb,
contigs_untrusted=previously_assembled_contigs,
out_fasta=outFasta,
mem_limit_gb=1)
self.assertGreater(os.path.getsize(outFasta), 0)
contig_lens = list(
sorted(
len(seq.seq)
for seq in Bio.SeqIO.parse(outFasta, 'fasta')))
#import sys
#print('test_assembly_with_previously_assembled_contigs_contigs_lens:', contig_lens, file=sys.stderr)
self.assertEqual(contig_lens, [
168, 170, 177, 180, 184, 187, 190, 191, 194, 197, 211, 243,
244, 247, 288, 328, 348, 430
])
