本文整理汇总了Python中edge.models.Genome.import_gff方法的典型用法代码示例。如果您正苦于以下问题：Python Genome.import_gff方法的具体用法？Python Genome.import_gff怎么用？Python Genome.import_gff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类edge.models.Genome的用法示例。
在下文中一共展示了Genome.import_gff方法的4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_import_feature_ending_at_last_base
# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import import_gff [as 别名]
def test_import_feature_ending_at_last_base(self):
data = """##gff-version 3
chrI\tTest\tchromosome\t1\t160\t.\t.\t.\tID=i1;Name=f1
chrI\tTest\tcds\t20\t28\t.\t-\t.\tID=i2;Name=f2
chrI\tTest\trbs\t20\t160\t.\t+\t.\tID=i3
###
##FASTA
>chrI
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCAT
"""
with tempfile.NamedTemporaryFile(mode='w+', delete=False) as f:
f.write(data)
f.close()
genome = Genome.import_gff('Foo', f.name)
os.unlink(f.name)
# verify chrI fragment
chrI = [fr.indexed_fragment() for fr in genome.fragments.all() if fr.name == 'chrI'][0]
self.assertEquals(len(chrI.sequence), 160)
# verify skips annotation on entire sequence
self.assertEquals(len(chrI.annotations()), 2)
self.assertEquals(chrI.annotations()[1].base_first, 20)
self.assertEquals(chrI.annotations()[1].base_last, 160)
self.assertEquals(chrI.annotations()[1].feature.name, 'i3') # no name, loaded ID
self.assertEquals(chrI.annotations()[1].feature.strand, 1)
self.assertEquals(chrI.annotations()[0].base_first, 20)
self.assertEquals(chrI.annotations()[0].base_last, 28)
self.assertEquals(chrI.annotations()[0].feature.name, 'f2')
self.assertEquals(chrI.annotations()[0].feature.strand, -1)示例2: test_import_gff_creates_fragments_and_annotate_features
# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import import_gff [as 别名]
def test_import_gff_creates_fragments_and_annotate_features(self):
data = """##gff-version 3
chrI\tTest\tchromosome\t1\t160\t.\t.\t.\tID=i1;Name=f1
chrI\tTest\tcds\t30\t80\t.\t-\t.\tID=i2;Name=f2
chrI\tTest\trbs\t20\t28\t.\t+\t.\tID=i3
chrII\tTest\tgene\t40\t60\t.\t-\t.\tID=f4;gene=g4
chrII\tTest\tgene\t20\t80\t.\t+\t.\tID=i5;Name=f5
###
##FASTA
>chrI
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCAT
>chrII
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCAT
"""
with tempfile.NamedTemporaryFile(mode='w+', delete=False) as f:
f.write(data)
f.close()
genome = Genome.import_gff('Foo', f.name)
os.unlink(f.name)
# created one fragment for each sequence in GFF file
self.assertItemsEqual([fr.name for fr in genome.fragments.all()], ['chrI', 'chrII'])
# verify chrI fragment
chrI = [fr.indexed_fragment() for fr in genome.fragments.all() if fr.name == 'chrI'][0]
self.assertEquals(len(chrI.sequence), 160)
# verify skips annotation on entire sequence
self.assertEquals(len(chrI.annotations()), 2)
self.assertEquals(chrI.annotations()[0].base_first, 20)
self.assertEquals(chrI.annotations()[0].base_last, 28)
self.assertEquals(chrI.annotations()[0].feature.name, 'i3') # no name, loaded ID
self.assertEquals(chrI.annotations()[0].feature.strand, 1)
self.assertEquals(chrI.annotations()[1].base_first, 30)
self.assertEquals(chrI.annotations()[1].base_last, 80)
self.assertEquals(chrI.annotations()[1].feature.name, 'f2')
self.assertEquals(chrI.annotations()[1].feature.strand, -1)
# verify chrII fragment
chrII = [fr.indexed_fragment() for fr in genome.fragments.all() if fr.name == 'chrII'][0]
self.assertEquals(len(chrII.sequence), 160)
# consecutive annotations merged even though they span multiple chunks
self.assertEquals(len(chrII.annotations()), 2)
self.assertEquals(chrII.annotations()[0].base_first, 20)
self.assertEquals(chrII.annotations()[0].base_last, 80)
self.assertEquals(chrII.annotations()[0].feature.name, 'f5')
self.assertEquals(chrII.annotations()[0].feature.strand, 1)
self.assertEquals(chrII.annotations()[1].base_first, 40)
self.assertEquals(chrII.annotations()[1].base_last, 60)
self.assertEquals(chrII.annotations()[1].feature.name, 'g4') # has gene, use gene name
self.assertEquals(chrII.annotations()[1].feature.strand, -1)示例3: import_gff
# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import import_gff [as 别名]
def import_gff(name, fn):
"""
Creates a new genome using the specified GFF file.
name: Name of genome
fn: path to GFF file
"""
from edge.models import Genome
if Genome.objects.filter(name=name).count() > 0:
raise Exception('There is already a genome named "%s"' % (name,))
g = Genome.import_gff(name, fn)
return g示例4: import_with_qualifiers
# 需要导入模块: from edge.models import Genome [as 别名]
# 或者: from edge.models.Genome import import_gff [as 别名]
def import_with_qualifiers(self, qualifiers):
data = """##gff-version 3
chrI\tTest\tcds\t30\t80\t.\t-\t.\t%s
###
##FASTA
>chrI
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCAT
""" % (qualifiers,)
with tempfile.NamedTemporaryFile(mode='w+', delete=False) as f:
f.write(data)
f.close()
self.genome = Genome.import_gff('Foo', f.name)
os.unlink(f.name)