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
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
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
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
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
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
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
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
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], )
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])
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')
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')