本文整理匯總了Python中edge.models.Genome.import_gff方法的典型用法代碼示例。如果您正苦於以下問題：Python Genome.import_gff方法的具體用法？Python Genome.import_gff怎麽用？Python Genome.import_gff使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類edge.models.Genome的用法示例。
在下文中一共展示了Genome.import_gff方法的4個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: test_import_feature_ending_at_last_base
# 需要導入模塊: from edge.models import Genome [as 別名]
# 或者: from edge.models.Genome import import_gff [as 別名]
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
# 需要導入模塊: from edge.models import Genome [as 別名]
# 或者: from edge.models.Genome import import_gff [as 別名]
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
# 需要導入模塊: from edge.models import Genome [as 別名]
# 或者: from edge.models.Genome import import_gff [as 別名]
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
# 需要導入模塊: from edge.models import Genome [as 別名]
# 或者: from edge.models.Genome import import_gff [as 別名]
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)