def test_amino_acid_residue_change_3_to_1_multiple():
## GIVEN a protein change on HGVS 3-letter format
a = "p.MetLys997ArgGlu"
## WHEN converting to 1-letter change string
r = amino_acid_residue_change_3_to_1(a)
## THEN the result is undefined
assert r is None
def test_amino_acid_residue_change_3_to_1_del():
## GIVEN a protein change on HGVS 3-letter format
a = "p.Phe2_Met46del"
## WHEN converting to 1-letter change string
r = amino_acid_residue_change_3_to_1(a)
## THEN the result is undefined
assert r is None
def test_amino_acid_residue_change_3_to_1_fs_ext():
## GIVEN a protein change on HGVS 3-letter format
a = "p.Arg544Glnext*17"
## WHEN converting to 1-letter change string
r = amino_acid_residue_change_3_to_1(a)
## THEN the result is undefined
assert r is None
def test_amino_acid_residue_change_3_to_1_synonymous():
## GIVEN a protein change on HGVS 3-letter format
a = "p.="
## WHEN converting to 1-letter change string
r = amino_acid_residue_change_3_to_1(a)
## THEN the result is correct
assert r is None
def test_amino_acid_residue_change_3_to_1_stop():
## GIVEN a protein change on HGVS 3-letter format
a = "p.Ser241Ter"
## WHEN converting to 1-letter change string
r = amino_acid_residue_change_3_to_1(a)
## THEN the result is correct
assert r == "S241*"
def cbioportal(hgnc_symbol, protein_sequence_name):
link = "https://www.cbioportal.org/ln?q={}:MUT%20%3D{}"
if not hgnc_symbol:
return None
if not protein_sequence_name:
return None
protein_change = amino_acid_residue_change_3_to_1(protein_sequence_name)
if not protein_change:
return None
return link.format(hgnc_symbol, protein_change)
def mycancergenome(hgnc_symbol, protein_sequence_name):
link = "https://www.mycancergenome.org/content/alteration/{}-{}"
if not hgnc_symbol:
return None
if not protein_sequence_name:
return None
protein_change = amino_acid_residue_change_3_to_1(protein_sequence_name)
if not protein_change:
return None
return link.format(hgnc_symbol, protein_change.lower())