Python Genome.import_gff示例

示例#1

文件： test_importer.py 项目： ginkgobioworks/edge

    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

文件： test_importer.py 项目： ginkgobioworks/edge

    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

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

文件： __init__.py 项目： ginkgobioworks/edge

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#5

文件： test_importer.py 项目： ginkgobioworks/edge

    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)

示例#6

    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)

示例#7

def import_gff(name, fn, output_dir='.'):
    """
    Creates a new genome using the specified GFF file.

    name: Name of genome
    fn: path to GFF file
    output_dir: string path to output directory for reference 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, dirn=output_dir)
    return g

示例#8

    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#9

    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)