Esempi in Python per peptide_from_transcript_variant

Esempio n. 1

def test_peptide_from_transcript_variant_RET():
    transcript_id = 'ENST00000340058'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            43617416,
            ref='T',
            alt='C',
            padding = None,
            max_length = None)
    assert peptide is not None

Esempio n. 2

File: test_transcript_variant.py Progetto: hammerlab/immuno

def test_peptide_from_transcript_variant_RET():
    transcript_id = 'ENST00000340058'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            43617416,
            ref='T',
            alt='C',
            padding = None,
            max_length = None)
    assert peptide is not None

Esempio n. 3

File: test_transcript_variant.py Progetto: hammerlab/immuno

def test_peptide_from_transcript_variant_VWA3A():
    transcript_id = 'ENST00000389397'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            22128096,
            ref='G',
            alt='A',
            padding = None,
            max_length = None)
    # expected mutation in the UTR to yield None
    assert peptide is None

Esempio n. 4

File: test_transcript_variant.py Progetto: hammerlab/immuno

def test_peptide_from_transcript_variant_CASP9():
    transcript_id = 'ENST00000333868'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            15820483,
            ref='C',
            alt='G',
            padding = None,
            max_length = None)
    assert peptide is not None
    assert len(peptide) == 416

Esempio n. 5

File: test_transcript_variant.py Progetto: hammerlab/immuno

def test_peptide_from_transcript_variant_PAR():

    transcript_id = 'ENST00000371279'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            55224569,
            ref='T',
            alt='G',
            padding = None,
            max_length = None)
    assert peptide is not None

Esempio n. 6

def test_peptide_from_transcript_variant_VWA3A():
    transcript_id = 'ENST00000389397'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            22128096,
            ref='G',
            alt='A',
            padding = None,
            max_length = None)
    # expected mutation in the UTR to yield None
    assert peptide is None

Esempio n. 7

def test_peptide_from_transcript_variant_CASP9():
    transcript_id = 'ENST00000333868'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            15820483,
            ref='C',
            alt='G',
            padding = None,
            max_length = None)
    assert peptide is not None
    assert len(peptide) == 416

Esempio n. 8

def test_peptide_from_transcript_variant_PAR():

    transcript_id = 'ENST00000371279'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            55224569,
            ref='T',
            alt='G',
            padding = None,
            max_length = None)
    assert peptide is not None

Esempio n. 9

File: test_dbnsfp_validation.py Progetto: hammerlab/immuno

def validate_transcript_mutation(row):
    transcript_id = row["ensembl_transcript"]
    print row
    peptide, start, stop, annot = transcript_variant.peptide_from_transcript_variant(
        transcript_id, row["position"], ref=row["ref"], alt=row["alt"], padding=None, max_length=None
    )
    assert peptide is not None
    aa_index = row["aapos"] - 1
    assert peptide[row["aapos"] - 1] == row["aaalt"], "Expected %s at amino acid pos %d but found %s" % (
        row["aaalt"],
        aa_index,
        peptide[aa_index],
    )

Esempio n. 10

def validate_transcript_mutation(row):
    transcript_id = row['ensembl_transcript']
    print row
    peptide, start, stop, annot = \
    transcript_variant.peptide_from_transcript_variant(
        transcript_id,
        row['position'],
        ref=row['ref'],
        alt=row['alt'],
        padding = None,
        max_length = None)
    assert peptide is not None
    aa_index = row['aapos'] - 1
    assert peptide[row['aapos'] - 1] == row['aaalt'], \
        "Expected %s at amino acid pos %d but found %s" % \
            (row['aaalt'], aa_index, peptide[aa_index])

Esempio n. 11

File: test_transcript_variant.py Progetto: hammerlab/immuno

def test_peptide_from_transcript_variant_CTNNB1():
    """
    test_peptide_from_transcript:

    Apply Cosmic mutation COSM27279
    transcript = 'ENST00000405570'
    pos: 41265571,
    ref : A, alt : T
    amino acids = Q -> H  @ pos 4 (mutation = Q4H)
    """
    transcript_id = 'ENST00000405570'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            41265571,
            ref='A',
            alt='T',
            padding = None,
            max_length = None)
    assert peptide is not None
    n = len(peptide)
    assert n == 781, (n, peptide)
    assert(peptide[3] == 'H')

Esempio n. 12

def test_peptide_from_transcript_variant_CTNNB1():
    """
    test_peptide_from_transcript:

    Apply Cosmic mutation COSM27279
    transcript = 'ENST00000405570'
    pos: 41265571,
    ref : A, alt : T
    amino acids = Q -> H  @ pos 4 (mutation = Q4H)
    """
    transcript_id = 'ENST00000405570'
    peptide, start, stop, annot = \
        transcript_variant.peptide_from_transcript_variant(
            transcript_id,
            41265571,
            ref='A',
            alt='T',
            padding = None,
            max_length = None)
    assert peptide is not None
    n = len(peptide)
    assert n == 781, (n, peptide)
    assert (peptide[3] == 'H')