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for line in openfile:
if line[0] == '>':
yield header, processSequences(sequences)
header = processHeaderLine(line)
sequences = list()
else:
sequences.append(line)
#Yield last entry
if sequences:
yield header, processSequences(sequences)"
1976,"def _extractFastaHeader(fastaHeader, parser=None, forceId=False):
""""""Parses a fasta header and returns extracted information in a dictionary.
Unless a custom parser is specified, a ``Pyteomics`` function is used, which
provides parsers for the formats of UniProtKB, UniRef, UniParc and UniMES
(UniProt Metagenomic and Environmental Sequences), described at
`www.uniprot.org <http://www.uniprot.org/help/fasta-headers>_`.
:param fastaHeader: str, protein entry header from a fasta file
:param parser: is a function that takes a fastaHeader string and returns a
dictionary, containing at least the key ""id"". If None the parser
function from pyteomics ``pyteomics.fasta.parse()`` is used.
:param forceId: bool, if True and no id can be extracted from the fasta
header the whole header sequence is used as a protein id instead of
raising an exception.
:returns: dict, describing a fasta header
""""""
if parser is None:
try:
headerInfo = pyteomics.fasta.parse(fastaHeader)
except pyteomics.auxiliary.PyteomicsError as pyteomicsError:
#If forceId is set True, it uses the whole header as an id
if forceId:
headerInfo = {'id': fastaHeader}
else:
raise pyteomicsError
else:
headerInfo = parser(fastaHeader)
return headerInfo"
1977,"def fastaParseSgd(header):
""""""Custom parser for fasta headers in the SGD format, see
www.yeastgenome.org.
:param header: str, protein entry header from a fasta file
:returns: dict, parsed header
""""""
rePattern = '([\S]+)\s([\S]+).+(\"".+\"")'
ID, name, description = re.match(rePattern, header).groups()
info = {'id':ID, 'name':name, 'description':description}
return info"
1978,"def _reprJSON(self):
""""""Returns a JSON serializable represenation of a ``PeptideSequence``
class instance. Use :func:`maspy.proteindb.PeptideSequence._fromJSON()`
to generate a new ``PeptideSequence`` instance from the return value.
:returns: a JSON serializable python object
""""""
return {'__PepSeq__': [self.sequence, self.missedCleavage,
self.isUnique, list(self.proteins),
self.proteinPositions]}"
1979,"def _fromJSON(cls, jsonobject):
""""""Generates a new instance of :class:`maspy.proteindb.PeptideSequence`
from a decoded JSON object (as generated by
:func:`maspy.proteindb.PeptideSequence._reprJSON()`).
:param jsonobject: decoded JSON object
:returns: a new instance of :class:`PeptideSequence`
""""""
newInstance = cls(jsonobject[0], jsonobject[1])
newInstance.isUnique = jsonobject[2]
newInstance.proteins = set(jsonobject[3])
newInstance.proteinPositions = jsonobject[4]
return newInstance"
1980,"def _reprJSON(self):
""""""Returns a JSON serializable represenation of a ``ProteinSequence``
class instance. Use :func:`maspy.proteindb.ProteinSequence._fromJSON()`
to generate a new ``ProteinSequence`` instance from the return value.
:returns: a JSON serializable python object
""""""
jsonDict = self.__dict__
jsonDict['uniquePeptides'] = list(jsonDict['uniquePeptides'])
jsonDict['sharedPeptides'] = list(jsonDict['sharedPeptides'])
return {'__ProtSeq__': jsonDict}"
1981,"def _fromJSON(cls, jsonobject):
""""""Generates a new instance of :class:`maspy.proteindb.ProteinSequence`
from a decoded JSON object (as generated by
:func:`maspy.proteindb.ProteinSequence._reprJSON()`).
:param jsonobject: decoded JSON object
:returns: a new instance of :class:`ProteinSequence`
""""""
newInstance = cls(None, None)