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if proteinId not in proteindb.proteins:
protein = ProteinSequence(proteinId, sequence)
protein.name = proteinName
protein.fastaHeader = header
protein.fastaInfo = headerInfo
proteindb.proteins[protein.id] = protein
#Perform the insilico digestion
_digestion = maspy.peptidemethods.digestInSilico(sequence, cleavageRule,
missedCleavage,
removeNtermM,
minLength, maxLength
)
#Add peptides to the protein database
for unmodPeptide, info in _digestion:
if ignoreIsoleucine:
unmodPeptideNoIsoleucine = unmodPeptide.replace('I', 'L')
if unmodPeptideNoIsoleucine in proteindb.peptides:
currPeptide = proteindb.peptides[unmodPeptideNoIsoleucine]
else:
currPeptide = PeptideSequence(unmodPeptideNoIsoleucine,
mc=info['missedCleavage']
)
proteindb.peptides[unmodPeptideNoIsoleucine] = currPeptide
if unmodPeptide not in proteindb.peptides:
proteindb.peptides[unmodPeptide] = currPeptide
else:
if unmodPeptide in proteindb.peptides:
currPeptide = proteindb.peptides[unmodPeptide]
else:
currPeptide = PeptideSequence(unmodPeptide,
mc=info['missedCleavage']
)
proteindb.peptides[unmodPeptide] = currPeptide
if proteinId not in currPeptide.proteins:
currPeptide.proteins.add(proteinId)
#TODO: change that a peptide can appear multiple times in a
# protein sequence.
currPeptide.proteinPositions[proteinId] = (info['startPos'],
info['endPos']
)
#Add peptide entries to the protein entries, define wheter a peptide can be
#uniquely assigend to a single protein (.isUnique = True).
for peptide, peptideEntry in viewitems(proteindb.peptides):
numProteinMatches = len(peptideEntry.proteins)
if numProteinMatches == 1:
peptideEntry.isUnique = True
elif numProteinMatches > 1:
peptideEntry.isUnique = False
else:
raise Exception('No protein matches in proteindb for peptide' +
'sequence: ' + peptide)
for proteinId in peptideEntry.proteins:
if peptideEntry.isUnique:
proteindb.proteins[proteinId].uniquePeptides.add(peptide)
else:
proteindb.proteins[proteinId].sharedPeptides.add(peptide)
#Check protein entries if the digestions generated at least one peptide that
#is uniquely assigned to the protein (.isUnique = True)
for proteinEntry in viewvalues(proteindb.proteins):
if len(proteinEntry.uniquePeptides) > 0:
proteinEntry.isUnique = True
else:
proteinEntry.isUnique = False
#Note: TODO, altough isoleucin is ignored, the protein entry should only
#show the actually present ILE / LEU occurence, not any possibilities
return proteindb"
1975,"def _readFastaFile(filepath):
""""""Read a FASTA file and yields tuples of 'header' and 'sequence' entries.
:param filepath: file path of the FASTA file
:yields: FASTA entries in the format ('header', 'sequence').
The 'header' string does not contain the '>' and trailing white spaces.
The 'sequence' string does not contain trailing white spaces, a '*' at
the end of the sequence is removed.
See also :func:`importProteinDatabase` and
:func:`maspy.peptidemethods.digestInSilico`.
""""""
processSequences = lambda i: ''.join([s.rstrip() for s in i]).rstrip('*')
processHeaderLine = lambda line: line[1:].rstrip()
with io.open(filepath) as openfile:
#Iterate through lines until the first header is encountered
try:
line = next(openfile)
while line[0] != '>':
line = next(openfile)
header = processHeaderLine(line)
sequences = list()
except StopIteration:
errorText = 'File does not contain fasta entries.'
raise maspy.errors.FileFormatError(errorText)