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 ])