def lookForRes(self, resCode):
""" Returns a Residue objected defined by the resCode (can be
three letter or one letter - we don't care!
"""
# if we're using a three letter code
if len(resCode) == 1:
if resCode in ONE_TO_THREE.keys():
return self.residue_table[ONE_TO_THREE[resCode]]
# if we're usin a one letter code
elif len(resCode) == 3:
if resCode in THREE_TO_ONE.keys():
return self.residue_table[resCode]
# if we got here we had an invalid AA code
raise ResTableException("Invalid amino acid code provided [" +
str(resCode) + "]")
def lookForRes(self, resCode):
""" Returns a Residue objected defined by the resCode (can be
three letter or one letter - we don't care!
"""
# if we're using a three letter code
if len(resCode) == 1:
if resCode in ONE_TO_THREE.keys():
return self.residue_table[ONE_TO_THREE[resCode]]
# if we're usin a one letter code
elif len(resCode) == 3:
if resCode in THREE_TO_ONE.keys():
return self.residue_table[resCode]
# if we got here we had an invalid AA code
raise ResTableException(
"Invalid amino acid code provided [" + str(resCode) + "]")
def __validSeq(self, sequence):
"""
Internal function which validates if a [region of]
a sequence is a valid protein sequence.
The validation skips spaces and numbers, but will raise an exception on any other character
"""
parsed_seq = ""
# for each residue in the sequence
for i in sequence:
# if the residue is not in the three letter code
if i not in ONE_TO_THREE.keys():
if i == " ":
# skip spaces
continue
elif i == "*":
# Add * for now but then validate at the end (* can be a stop codon)
parsed_seq = parsed_seq + i
continue
elif i in "1234567890":
warning_message(
"Found '" + i + "' in sequence, stripping out and ignoring...")
# strip out numbers (useful for copy/pasted FASTA formats)
continue
else:
raise SequenceFileParserException(
"\n\nERROR: Invalid sequence file, found [" +
i +
"] in sequence region\n\n" +
sequence +
"\n\n")
# if the residue *is* one of the 20 AAs then append to the growing
# sequence
else:
parsed_seq = parsed_seq + i
return parsed_seq
def __validSeq(self, sequence):
"""
Internal function which validates if a [region of]
a sequence is a valid protein sequence.
The validation skips spaces and numbers, but will raise an exception on any other character
"""
parsed_seq = ""
# for each residue in the sequence
for i in sequence:
# if the residue is not in the three letter code
if i not in ONE_TO_THREE.keys():
if i == " ":
# skip spaces
continue
elif i in "1234567890":
warning_message(
"Found '" + i + "' in sequence, stripping out and ignoring...")
# strip out numbers (useful for copy/pasted FASTA formats)
continue
else:
raise SequenceFileParserException(
"\n\nERROR: Invalid sequence file, found [" +
i +
"] in sequence region\n\n" +
sequence +
"\n\n")
# if the residue *is* one of the 20 AAs then append to the growing
# sequence
else:
parsed_seq = parsed_seq + i
return parsed_seq
