def setUp(self):
# generate a Protein for use in the tests of this class
self.single_protein = Protein("ASDERWQTGHKILPMNVFCY", gene_id='gene 1', transcript_id='someID')
# generate a set of Proteins for use in the tests of this class
self.prot_set = list()
self.prot_set.append(Protein("IIIVRC", gene_id='gene 1', transcript_id='set entry 1'))
self.prot_set.append(Protein("VRCVR", gene_id='gene 1', transcript_id='set entry 2'))
self.prot_set.append(Protein("IIVRCIT", gene_id='gene 1', transcript_id='set entry 3'))
self.prot_set.append(Protein("IVRC", gene_id='gene 1', transcript_id='set entry 4'))
def setUp(self):
self.seqs = [
Peptide("SYFPEISYFP"),
Protein("IHTIEPFYSIHTIEPFYSIHTIEPFYSIHTIEPFYSIHTIEPFYS", "ID-01",
"FOXP3")
]
self.fragments = [Peptide("FSYFPEITHIR"), Peptide("FIHTIEPFYSR")]
def setUp(self):
self.peptides = [Peptide("SYFPEITHI"), Peptide("IHTIEPFYS")]
testsequences_file = pkg_resources.resource_filename(
'Fred2', path.join('Data', 'examples', 'testSequences.fasta'))
with open(testsequences_file, "rU") as handle:
records = list(SeqIO.parse(handle, "fasta"))
prot_set = [Protein(str(r.seq)) for r in records]
unique_test_pep_set = generate_peptides_from_proteins(prot_set, 9)
self.selfpeptides = [str(x) for x in unique_test_pep_set]
small_prot_set = [
Protein(
"MKERRIDMKEKNVKAKAPNKKVLGLTTKIFIALLAGAILGIVLCYLVPDSSFKKDVIVEGILYVIGQGFIRLMKMLVVPLVFCSLVCGSMAIGDTKKLGTVGVRTLAFYLATTALAVVALGVGNLINPGVGLDMSAIQSSAASVETMEATSLTDTILNIIPDNPINSLASGSMLQVIVFALIVGVILAKMGERAETVANFFSQFNDIMMEMTMMIMSLAPIGVFCLISRTFANIGFSAFIPLAKYMIGVLLALAIQCFGVYQILLKIFTGLNPIRFIKKFFPVMAFAFSTATSNATIPMSIDTLSKKVGVSKKISSFTIPLGATINMDGTSIMQGVAVVFAAQAFGIHLTPMDYVTVIGTATLASVGTAGVPSVGLVTLTMVFNSVGLPVEAIGLIMGIDRILDMTRTAVNITGDAVCTTIVAHQNGALDKKVFNETE"
),
Protein(
"MLKVWIAGASGQIGRALNDVLDPMQIEALNTDLDELDITDTDEVINFGTVNRPDVIINCTGITDTDECEANPEHAYRVNALGARNLSIVARKCGSKIVQLSTDDVFDGQSKKPYTEFDDTNPLTVYGRSKRAGENYVKEFTHKHFVIRSNWVYGHGGHNFVNRVLAAAEAGNGLSVASDQFGSPTSAKDLAKMIMYLISTNEYGTYHVTCRGVCSRYEFAQEILKLAGKDIELRAVPTEQSDLSAVRPPYAVLDNFILRIIEVYDMPDWKESLKEYMDERTED"
)
]
small_unique_test_pep_set = generate_peptides_from_proteins(
small_prot_set, 9)
self.fewselfpeptides = [str(x) for x in small_unique_test_pep_set]
def generate_proteins_from_transcripts(transcripts, table='Standard', stop_symbol='*', to_stop=True, cds=False):
"""
Enables the translation from a :class:`~Fred2.Core.Transcript.Transcript` to a
:class:`~Fred2.Core.Protein.Protein` instance. The result is a generator.
The result is a generator.
:param transcripts: A list of or a single transcripts to translate
:type transcripts: list(:class:`~Fred2.Core.Transcript.Transcript`) or :class:`~Fred2.Core.Transcript.Transcript`
:param str table: Which codon table to use? This can be either a name (string), an NCBI identifier (integer),
or a CodonTable object (useful for non-standard genetic codes). Defaults to the 'Standard'
table
:param str stop_symbol: Single character string, what to use for any terminators, defaults to the asterisk, '*'
:param bool to_stop: Translates sequence and passes any stop codons if False (default True)(translated as the
specified stop_symbol). If True, translation is terminated at the first in frame stop
codon (and the stop_symbol is not appended to the returned protein sequence)
:param bool cds: Boolean, indicates this is a complete CDS. If True, this checks the sequence starts with a
valid alternative start codon (which will be translated as methionine, M), that the sequence
length is a multiple of three, and that there is a single in frame stop codon at the end
(this will be excluded from the protein sequence, regardless of the to_stop option).
If these tests fail, an exception is raised
:returns: The protein that corresponds to the transcript
:rtype: Generator(:class:`~Fred2.Core.Protein.Protein`)
:raises ValueError: If incorrect table argument is pasted
:raises TranslationError: If sequence is not multiple of three, or first codon is not a start codon, or last
codon ist not a stop codon, or an extra stop codon was found in frame, or codon is
non-valid
"""
if isinstance(transcripts, Transcript):
transcripts = [transcripts]
for t in transcripts:
if not isinstance(t, Transcript):
raise ValueError("An element of specified input is not of type Transcript")
# translate to a protein sequence
#if len(str(self)) % 3 != 0:
# raise ValueError('ERROR while translating: lenght of transcript %s is no multiple of 3, the transcript is:\n %s' % (self.transcript_id, self))
#TODO warn if intrasequence stops - biopython warns if % 3 != 0
prot_seq = str(t.translate(table=table, stop_symbol=stop_symbol, to_stop=to_stop, cds=cds))
new_vars = dict()
for pos, var in t.vars.iteritems():
if not var.isSynonymous:
prot_pos = pos // 3
new_vars.setdefault(prot_pos, []).append(var)
gene_id = t.gene_id
yield Protein(prot_seq, gene_id, t.transcript_id, t, new_vars)
def extractEpitopeInformationFromMSA(input, epitope_length):
error = ''
NONE = 0
ANTIGEN_HEADER = 1
SEQUENCE_HEADER = 2
SEQUENCE = 3
last_read = NONE
antigen = ''
current_sequence = ''
sequences = []
consensus_info = {}
consensuses = {}
epitope_info = []
antigens = []
conservation = {}
with open(input, "r") as f:
for line in f:
line = line.strip()
if line == '' or line[0] == '#':
continue
# print 'in extract msa info',line
if line.startswith('>'):
if last_read == NONE or last_read == SEQUENCE:
if last_read == SEQUENCE: # done with previous antigen
sequences.append(current_sequence)
current_sequence = ''
antigen = line[2:].strip()
last_read = SEQUENCE_HEADER
else: # wrong format
error = "Input format does not comply with required MSA format."
break
elif line[0] == '>' and antigen != '':
if last_read == ANTIGEN_HEADER or last_read == SEQUENCE:
if last_read == SEQUENCE:
sequences.append(current_sequence)
current_sequence = ''
last_read = SEQUENCE_HEADER
else: # sequence
if not isValidMSASequence(line) and antigen != '':
error = "Invalid amino acid sequence given for antigen " + antigen + ". "
break
if last_read == SEQUENCE_HEADER or last_read == SEQUENCE:
# current_sequence += line[:-1]
current_sequence += line
last_read = SEQUENCE
else:
error = "Input format does not comply with required MSA format."
break
if error == '':
if last_read == SEQUENCE:
sequences.append(current_sequence)
consensus = determineConsensusFromMSA(sequences)
if consensus[0] != '':
consensuses[antigen] = consensus[0].upper()
consensus_info.setdefault(antigen, []).append(
(Protein(consensus[0].upper(), antigen, antigen), consensus[1]))
else: # different sequence lengths
error = "MSA sequences of antigen " + antigen + " are of different lengths."
else:
error = "Input format does not comply with required MSA format."
if error == '':
(error, conservation) = extractEpitopesAndConservationFromConsensus(consensus_info, epitope_length)
# print "infos form extractEpitopesAndConservationFromConsensus", conservation
return (error, conservation, consensuses)