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Python Genome.save方法代码示例

本文整理汇总了Python中edge.models.Genome.save方法的典型用法代码示例。如果您正苦于以下问题:Python Genome.save方法的具体用法?Python Genome.save怎么用?Python Genome.save使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在edge.models.Genome的用法示例。


在下文中一共展示了Genome.save方法的11个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: test_blast_aligns_sequence_to_antisense_strand

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_blast_aligns_sequence_to_antisense_strand(self):
        s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
        g1 = Genome(name='Foo')
        g1.save()
        f1 = Fragment.create_with_sequence('Bar', s1)
        Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()

        try:
            os.unlink(fragment_fasta_fn(f1))
        except:
            pass
        build_all_genome_dbs(refresh=True)

        query = str(Seq(s1[6:20]).reverse_complement())+'tttttttttt'

        res = self.client.post('/edge/genomes/%s/blast/' % g1.id,
                               data=json.dumps(dict(program='blastn', query=query)),
                               content_type='application/json')
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)

        # only returns hit from genome
        self.assertEquals(len(d), 1)
        self.assertEquals(d[0]['fragment_id'], f1.id)
        self.assertEquals(d[0]['query_start'], 1)
        self.assertEquals(d[0]['query_end'], 14)
        self.assertEquals(d[0]['subject_start'], 20)
        self.assertEquals(d[0]['subject_end'], 7)
开发者ID:cavedweller,项目名称:edge,代码行数:30,代码来源:test_blast.py

示例2: test_finds_sequence_on_specified_genome

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_finds_sequence_on_specified_genome(self):
        s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
        s2 = 'agcgtcgatgcatgagtcgatcggcagtcgtgtagtcgtcgtatgcgtta'
        g1 = Genome(name='Foo')
        g1.save()
        f1 = Fragment.create_with_sequence('Bar', s1)
        f2 = Fragment.create_with_sequence('Baz', s2)
        Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
        Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()

        g2 = Genome(name='Far')
        g2.save()
        f3 = Fragment.create_with_sequence('Bar', s1)
        Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()

        try:
            os.unlink(fragment_fasta_fn(f1))
            os.unlink(fragment_fasta_fn(f2))
            os.unlink(fragment_fasta_fn(f3))
        except:
            pass
        build_all_genome_dbs(refresh=True)
        g1 = Genome.objects.get(pk=g1.id)

        query = s1[6:20] + 'aaaaaaaaa'
        r = blast_genome(g1, 'blastn', query)
        # only returns hit from genome
        self.assertEquals(len(r), 1)
        self.assertEquals(r[0].fragment_id, f1.id)
        self.assertEquals(r[0].query_start, 1)
        self.assertEquals(r[0].query_end, 14)
        self.assertEquals(r[0].subject_start, 7)
        self.assertEquals(r[0].subject_end, 20)
        self.assertEquals(r[0].strand(), 1)
开发者ID:ginkgobioworks,项目名称:edge,代码行数:36,代码来源:test_blast.py

示例3: test_finds_genomes_with_name

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_finds_genomes_with_name(self):
        from edge.models import Genome

        a = Genome(name='Foo')
        a.save()
        Genome(name='Bar %s' % a.id).save()

        # no filter, return both genomes
        res = self.client.get('/edge/genomes/')
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])

        # finds genome by ID and query
        res = self.client.get('/edge/genomes/?q=%s' % a.id)
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertItemsEqual([g['name'] for g in d], ['Foo', 'Bar %s' % a.id])

        # finds one
        res = self.client.get('/edge/genomes/?q=oo')
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertItemsEqual([g['name'] for g in d], ['Foo'])

        # finds none
        res = self.client.get('/edge/genomes/?q=ooo')
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertItemsEqual([g['name'] for g in d], [])
开发者ID:Chris7,项目名称:edge,代码行数:32,代码来源:test_views.py

示例4: build_genome

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
 def build_genome(self, circular, *templates):
     g = Genome(name='Foo')
     g.save()
     for seq in templates:
         f = Fragment.create_with_sequence('Bar', seq, circular=circular)
         Genome_Fragment(genome=g, fragment=f, inherited=False).save()
         try:
             os.unlink(fragment_fasta_fn(f))
         except:
             pass
     build_all_genome_dbs(refresh=True)
     return Genome.objects.get(pk=g.id)
开发者ID:Chris7,项目名称:edge,代码行数:14,代码来源:test_primer.py

示例5: test_finds_genomes_with_specified_fragment_ids

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_finds_genomes_with_specified_fragment_ids(self):
        from edge.models import Genome, Fragment, Genome_Fragment

        g1 = Genome(name='Foo')
        g1.save()
        g2 = Genome(name='Bar')
        g2.save()
        f1 = Fragment(circular=True, name='FooF1')
        f1.save()
        f2 = Fragment(circular=True, name='FooF2')
        f2.save()
        f3 = Fragment(circular=True, name='FooF3', parent=f2)
        f3.save()
        Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
        Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()
        Genome_Fragment(genome=g2, fragment=f1, inherited=True).save()
        Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()

        # no filter, return both genomes
        res = self.client.get('/edge/genomes/')
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertItemsEqual([g['id'] for g in d], [g1.id, g2.id])

        # looking for f1 and f2
        res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f1.id, f2.id))
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertItemsEqual([g['id'] for g in d], [g1.id])

        # looking for f1 and f3
        res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f1.id, f3.id))
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertItemsEqual([g['id'] for g in d], [g2.id])

        # looking for f2 and f3
        res = self.client.get('/edge/genomes/?f=%d&f=%d' % (f2.id, f3.id))
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertEquals(d, [])

        # looking for f1
        res = self.client.get('/edge/genomes/?f=%d' % (f1.id,))
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertEquals(d, [])

        # bad input, return []
        res = self.client.get('/edge/genomes/?f=[1,2,3]')
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertEquals(d, [])
开发者ID:Chris7,项目名称:edge,代码行数:55,代码来源:test_views.py

示例6: test_does_not_return_genomic_fragments

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_does_not_return_genomic_fragments(self):
        from edge.models import Genome, Genome_Fragment

        res = self.client.get('/edge/fragments/')
        self.assertEquals(res.status_code, 200)
        self.assertEquals(len(json.loads(res.content)), 1)

        g = Genome(name='Foo')
        g.save()
        Genome_Fragment(genome=g, fragment_id=self.fragment_id, inherited=False).save()

        res = self.client.get('/edge/fragments/')
        self.assertEquals(res.status_code, 200)
        self.assertEquals(len(json.loads(res.content)), 0)
开发者ID:Chris7,项目名称:edge,代码行数:16,代码来源:test_views.py

示例7: test_blast_finds_sequence_on_specified_genome

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_blast_finds_sequence_on_specified_genome(self):
        s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
        s2 = 'agcgtcgatgcatgagtcgatcggcagtcgtgtagtcgtcgtatgcgtta'
        g1 = Genome(name='Foo')
        g1.save()
        f1 = Fragment.create_with_sequence('Bar', s1)
        f2 = Fragment.create_with_sequence('Baz', s2)
        Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()
        Genome_Fragment(genome=g1, fragment=f2, inherited=False).save()

        g2 = Genome(name='Far')
        g2.save()
        f3 = Fragment.create_with_sequence('Bar', s1)
        Genome_Fragment(genome=g2, fragment=f3, inherited=False).save()

        try:
            os.unlink(fragment_fasta_fn(f1))
            os.unlink(fragment_fasta_fn(f2))
            os.unlink(fragment_fasta_fn(f3))
        except:
            pass
        build_all_genome_dbs(refresh=True)

        query = s1[6:20]+'aaaaaaaaa'

        res = self.client.post('/edge/genomes/%s/blast/' % g1.id,
                               data=json.dumps(dict(program='blastn', query=query)),
                               content_type='application/json')
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)

        # only returns hit from genome
        self.assertEquals(len(d), 1)
        self.assertEquals(d[0]['fragment_id'], f1.id)
        self.assertEquals(d[0]['query_start'], 1)
        self.assertEquals(d[0]['query_end'], 14)
        self.assertEquals(d[0]['subject_start'], 7)
        self.assertEquals(d[0]['subject_end'], 20)

        # blast in other genome works too
        res = self.client.post('/edge/genomes/%s/blast/' % g2.id,
                               data=json.dumps(dict(program='blastn', query=query)),
                               content_type='application/json')
        self.assertEquals(res.status_code, 200)
        d = json.loads(res.content)
        self.assertEquals(len(d), 1)
        self.assertEquals(d[0]['fragment_id'], f3.id)
开发者ID:cavedweller,项目名称:edge,代码行数:49,代码来源:test_blast.py

示例8: test_does_not_return_duplicate_hits_for_circular_fragments

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_does_not_return_duplicate_hits_for_circular_fragments(self):
        s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
        g1 = Genome(name='Foo')
        g1.save()
        f1 = Fragment.create_with_sequence('Bar', s1, circular=True)
        Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()

        try:
            os.unlink(fragment_fasta_fn(f1))
        except:
            pass
        build_all_genome_dbs(refresh=True)
        g1 = Genome.objects.get(pk=g1.id)

        query = s1[5:20] + 'tttttttttt'
        r = blast_genome(g1, 'blastn', query)
        self.assertEquals(len(r), 1)
开发者ID:ginkgobioworks,项目名称:edge,代码行数:19,代码来源:test_blast.py

示例9: test_does_not_align_sequence_across_boundry_for_non_circular_fragment

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_does_not_align_sequence_across_boundry_for_non_circular_fragment(self):
        s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
        g1 = Genome(name='Foo')
        g1.save()
        f1 = Fragment.create_with_sequence('Bar', s1, circular=False)
        Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()

        try:
            os.unlink(fragment_fasta_fn(f1))
        except:
            pass
        build_all_genome_dbs(refresh=True)
        g1 = Genome.objects.get(pk=g1.id)

        query = (s1[-10:] + s1[0:10]) + 'tttttttttt'
        res = blast_genome(g1, 'blastn', query)

        for r in res:
            self.assertEquals(r.subject_start > 0 and r.subject_start <= len(s1), True)
            self.assertEquals(r.subject_end > 0 and r.subject_end <= len(s1), True)
开发者ID:ginkgobioworks,项目名称:edge,代码行数:22,代码来源:test_blast.py

示例10: test_aligns_sequence_to_antisense_strand

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_aligns_sequence_to_antisense_strand(self):
        s1 = 'atcggtatcttctatgcgtatgcgtcatgattatatatattagcggcatg'
        g1 = Genome(name='Foo')
        g1.save()
        f1 = Fragment.create_with_sequence('Bar', s1)
        Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()

        try:
            os.unlink(fragment_fasta_fn(f1))
        except:
            pass
        build_all_genome_dbs(refresh=True)
        g1 = Genome.objects.get(pk=g1.id)

        query = str(Seq(s1[6:20]).reverse_complement()) + 'tttttttttt'
        r = blast_genome(g1, 'blastn', query)
        self.assertEquals(len(r), 1)
        self.assertEquals(r[0].fragment_id, f1.id)
        self.assertEquals(r[0].query_start, 1)
        self.assertEquals(r[0].query_end, 14)
        self.assertEquals(r[0].subject_start, 20)
        self.assertEquals(r[0].subject_end, 7)
        self.assertEquals(r[0].strand(), -1)
开发者ID:ginkgobioworks,项目名称:edge,代码行数:25,代码来源:test_blast.py

示例11: test_aligns_sequence_across_boundry_for_circular_fragment

# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import save [as 别名]
    def test_aligns_sequence_across_boundry_for_circular_fragment(self):
        s1 = 'atcggtatctactatgcgtatgcgtcatgattatatatattagcggcatg'
        g1 = Genome(name='Foo')
        g1.save()
        f1 = Fragment.create_with_sequence('Bar', s1, circular=True)
        Genome_Fragment(genome=g1, fragment=f1, inherited=False).save()

        try:
            os.unlink(fragment_fasta_fn(f1))
        except:
            pass
        build_all_genome_dbs(refresh=True)
        g1 = Genome.objects.get(pk=g1.id)

        query = (s1[-10:] + s1[0:10]) + 'ttttttttttt'
        res = blast_genome(g1, 'blastn', query)

        # we are not removing redundant matches when matching across circular
        # boundaries, since blasting across circular boundary of a genome is a
        # rare case. so in this particular case, you will find two results, one
        # for the end of the query at the start of the genome, one for across
        # the circular boundary.

        found = False
        for r in res:
            if r.query_start == 1 and r.query_end == 20:
                self.assertEquals(r.fragment_id, f1.id)
                self.assertEquals(r.query_start, 1)
                self.assertEquals(r.query_end, 20)
                self.assertEquals(r.subject_start, len(s1) - 10 + 1)
                self.assertEquals(r.subject_end, len(s1) + 10)
                self.assertEquals(r.fragment_length, len(s1))
                self.assertEquals(r.strand(), 1)
                found = True
                break
        self.assertEquals(found, True)
开发者ID:ginkgobioworks,项目名称:edge,代码行数:38,代码来源:test_blast.py


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