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_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])