def test_satisfies1(self):
file1 = StringIO("""
#=GENOME_DIFF 1.0
SNP 1 12 REL606 72313 C aa_new_seq=G aa_position=92 aa_ref_seq=D codon_new_seq=GGC codon_number=92 codon_position=2 codon_ref_seq=GAC gene_name=araA gene_position=275 gene_product=L-arabinose isomerase gene_strand=< genes_overlapping=araA locus_tag=ECB_00064 locus_tags_overlapping=ECB_00064 mutation_category=snp_nonsynonymous position_end=72313 position_start=72313 snp_type=nonsynonymous transl_table=11
""".strip())
document1 = GenomeDiff.read(file1)
file2 = StringIO("""
#=GENOME_DIFF 1.0
SNP 1 34 REL606 72313 C aa_new_seq=G aa_position=92 aa_ref_seq=D codon_new_seq=GGC codon_number=92 codon_position=2 codon_ref_seq=GAC gene_name=araA gene_position=275 gene_product=L-arabinose isomerase gene_strand=< genes_overlapping=araA locus_tag=ECB_00064 locus_tags_overlapping=ECB_00064 mutation_category=snp_nonsynonymous position_end=72313 position_start=72313 snp_type=nonsynonymous transl_table=11
""".strip())
document2 = GenomeDiff.read(file2)
self.assertEqual(document1.mutations[0].satisfies("gene_name==araA"),
True)
self.assertEqual(
document1.mutations[0].satisfies(
"mutation_category==snp_nonsynonymous"), True)
self.assertEqual(
document1.mutations[0].satisfies("position_start>=50.5"), True)
self.assertEqual(
document1.mutations[0].satisfies("position_start<=10000000.2"),
True)
document2.remove("gene_name==rrlA")
print()
print(document1.mutations)
print()
print(document2.mutations)
self.assertEqual(document1.mutations, document2.mutations)
document2.remove("gene_name==araA")
self.assertEqual(document2.mutations, [])
def test_cmp2(self):
file1 = StringIO("""
#=GENOME_DIFF 1.0
SNP 1 12 REL606 72313 C aa_new_seq=G aa_position=92 aa_ref_seq=D codon_new_seq=GGC codon_number=92 codon_position=2 codon_ref_seq=GAC gene_name=araA gene_position=275 gene_product=L-arabinose isomerase gene_strand=< genes_overlapping=araA locus_tag=ECB_00064 locus_tags_overlapping=ECB_00064 mutation_category=snp_nonsynonymous position_end=72313 position_start=72313 snp_type=nonsynonymous transl_table=11
""".strip())
document1 = GenomeDiff.read(file1)
file2 = StringIO("""
#=GENOME_DIFF 1.0
SNP 1 34 REL606 72313 C aa_new_seq=G aa_position=92 aa_ref_seq=D codon_new_seq=GGC codon_number=92 codon_position=2 codon_ref_seq=GAC gene_name=araA gene_position=275 gene_product=L-arabinose isomerase gene_strand=< genes_overlapping=araA locus_tag=ECB_00064 locus_tags_overlapping=ECB_00064 mutation_category=snp_nonsynonymous position_end=72313 position_start=72313 snp_type=nonsynonymous transl_table=11
""".strip())
document2 = GenomeDiff.read(file2)
self.assertEqual(document1.mutations,document2.mutations)
def test_document(self):
file = StringIO("""
#=GENOME_DIFF 1.0
#=AUTHOR test
SNP 1 23423 NC_000913 223 A
RA 2 NC_000913 223 0 G A
""".strip())
document = GenomeDiff.read(file)
self.assertEqual({
'AUTHOR': 'test',
'GENOME_DIFF': '1.0'
}, document.metadata)
snp_record = Record('SNP',
1,
document, [23423],
seq_id='NC_000913',
new_seq='A',
position=223)
ra_record = Record('RA',
2,
document,
None,
position=223,
seq_id='NC_000913',
insert_position=0,
new_base='A',
ref_base='G')
self.assertEqual([snp_record], document.mutations)
self.assertEqual([ra_record], document.evidence)
self.assertEqual(snp_record, document[1])
self.assertEqual(ra_record, document[2])
def test_resolve(self):
file = StringIO("""
#=GENOME_DIFF 1.0
#=AUTHOR test
SNP 1 2 NC_000913 223 A
RA 2 NC_000913 223 0 G A
""".strip())
document = GenomeDiff.read(file)
self.assertEqual(document[1].parents, [document[2]])
def test_resolve(self):
file = StringIO("""
#=GENOME_DIFF 1.0
#=AUTHOR test
SNP 1 2 NC_000913 223 A
RA 2 NC_000913 223 0 G A
""".strip())
document = GenomeDiff.read(file)
self.assertEqual(document[1].parents, [document[2]])
def test_cmp1(self):
file1 = StringIO("""
#=GENOME_DIFF 1.0
#=CREATED 20:02:17 23 Jan 2019
#=PROGRAM breseq 0.33.2
#=COMMAND breseq -r LCA.gff3 sequence-data/DM0 evolved re-runs (Rohan)/ZDBp889_R1.fastq.gz sequence-data/DM0 evolved re-runs (Rohan)/ZDBp889_R2.fastq.gz sequence-data/ZDBp889_reads.fastq -o consensus/ZDBp889
#=REFSEQ LCA.gff3
#=READSEQ sequence-data/DM0 evolved re-runs (Rohan)/ZDBp889_R1.fastq.gz
#=READSEQ sequence-data/DM0 evolved re-runs (Rohan)/ZDBp889_R2.fastq.gz
#=READSEQ sequence-data/ZDBp889_reads.fastq
#=CONVERTED-BASES 644779377
#=CONVERTED-READS 14448149
#=INPUT-BASES 645034321
#=INPUT-READS 14455411
#=MAPPED-BASES 602854657
#=MAPPED-READS 13788351
SNP 1 34 REL606 72313 C
""".strip())
document1 = GenomeDiff.read(file1)
file2 = StringIO("""
#=GENOME_DIFF 1.0
#=CREATED 16:49:49 23 Jan 2019
#=PROGRAM breseq 0.33.2
#=COMMAND breseq -r LCA.gff3 sequence-data/DM0 evolved re-runs (Rohan)/ZDB67_R1.fastq.gz sequence-data/DM0 evolved re-runs (Rohan)/ZDB67_R2.fastq.gz -o consensus/ZDB67
#=REFSEQ LCA.gff3
#=READSEQ sequence-data/DM0 evolved re-runs (Rohan)/ZDB67_R1.fastq.gz
#=READSEQ sequence-data/DM0 evolved re-runs (Rohan)/ZDB67_R2.fastq.gz
#=CONVERTED-BASES 114566968
#=CONVERTED-READS 419781
#=INPUT-BASES 114567554
#=INPUT-READS 419783
#=MAPPED-BASES 92472620
#=MAPPED-READS 339813
SNP 1 12 REL606 72313 C
""".strip())
document2 = GenomeDiff.read(file2)
self.assertEqual(document1.mutations,document2.mutations)
def test_document(self):
file = StringIO("""
#=GENOME_DIFF 1.0
#=AUTHOR test
SNP 1 23423 NC_000913 223 A
RA 2 NC_000913 223 0 G A
""".strip())
document = GenomeDiff.read(file)
self.assertEqual({'AUTHOR': 'test', 'GENOME_DIFF': '1.0'}, document.metadata)
snp_record = Record('SNP', 1, document, [23423], seq_id='NC_000913', new_seq='A', position=223)
ra_record = Record('RA', 2, document, None, position=223, seq_id='NC_000913', insert_position=0, new_base='A',
ref_base='G')
self.assertEqual([snp_record], document.mutations)
self.assertEqual([ra_record], document.evidence)
self.assertEqual(snp_record, document[1])
self.assertEqual(ra_record, document[2])