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author | galaxyp |
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date | Mon, 22 Jan 2018 13:59:27 -0500 |
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# Copyright 2012 Anton Goloborodko, Lev Levitsky # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. import itertools as it import re from collections import deque def cleave(sequence, rule, missed_cleavages=0, min_length=None): """Cleaves a polypeptide sequence using a given rule. Parameters ---------- sequence : str The sequence of a polypeptide. .. note:: The sequence is expected to be in one-letter uppercase notation. Otherwise, some of the cleavage rules in :py:data:`expasy_rules` will not work as expected. rule : str or compiled regex A regular expression describing the site of cleavage. It is recommended to design the regex so that it matches only the residue whose C-terminal bond is to be cleaved. All additional requirements should be specified using `lookaround assertions <http://www.regular-expressions.info/lookaround.html>`_. :py:data:`expasy_rules` contains cleavage rules for popular cleavage agents. missed_cleavages : int, optional Maximum number of allowed missed cleavages. Defaults to 0. min_length : int or None, optional Minimum peptide length. Defaults to :py:const:`None`. ..note :: This checks for string length, which is only correct for one-letter notation and not for full *modX*. Use :py:func:`length` manually if you know what you are doing and apply :py:func:`cleave` to *modX* sequences. Returns ------- out : set A set of unique (!) peptides. Examples -------- >>> cleave('AKAKBK', expasy_rules['trypsin'], 0) == {'AK', 'BK'} True >>> cleave('GKGKYKCK', expasy_rules['trypsin'], 2) == \ {'CK', 'GKYK', 'YKCK', 'GKGK', 'GKYKCK', 'GK', 'GKGKYK', 'YK'} True """ return set(_cleave(sequence, rule, missed_cleavages, min_length)) def _cleave(sequence, rule, missed_cleavages=0, min_length=None): """Like :py:func:`cleave`, but the result is a list. Refer to :py:func:`cleave` for explanation of parameters. """ peptides = [] ml = missed_cleavages+2 trange = range(ml) cleavage_sites = deque([0], maxlen=ml) cl = 1 for i in it.chain([x.end() for x in re.finditer(rule, sequence)], [None]): cleavage_sites.append(i) if cl < ml: cl += 1 for j in trange[:cl-1]: seq = sequence[cleavage_sites[j]:cleavage_sites[-1]] if seq: if min_length is None or len(seq) >= min_length: peptides.append(seq) return peptides def num_sites(sequence, rule, **kwargs): """Count the number of sites where `sequence` can be cleaved using the given `rule` (e.g. number of miscleavages for a peptide). Parameters ---------- sequence : str The sequence of a polypeptide. rule : str or compiled regex A regular expression describing the site of cleavage. It is recommended to design the regex so that it matches only the residue whose C-terminal bond is to be cleaved. All additional requirements should be specified using `lookaround assertions <http://www.regular-expressions.info/lookaround.html>`_. labels : list, optional A list of allowed labels for amino acids and terminal modifications. Returns ------- out : int Number of cleavage sites. """ return len(_cleave(sequence, rule, **kwargs)) - 1 expasy_rules = { 'arg-c': r'R', 'asp-n': r'\w(?=D)', 'bnps-skatole': r'W', 'caspase 1': r'(?<=[FWYL]\w[HAT])D(?=[^PEDQKR])', 'caspase 2': r'(?<=DVA)D(?=[^PEDQKR])', 'caspase 3': r'(?<=DMQ)D(?=[^PEDQKR])', 'caspase 4': r'(?<=LEV)D(?=[^PEDQKR])', 'caspase 5': r'(?<=[LW]EH)D', 'caspase 6': r'(?<=VE[HI])D(?=[^PEDQKR])', 'caspase 7': r'(?<=DEV)D(?=[^PEDQKR])', 'caspase 8': r'(?<=[IL]ET)D(?=[^PEDQKR])', 'caspase 9': r'(?<=LEH)D', 'caspase 10': r'(?<=IEA)D', 'chymotrypsin high specificity': r'([FY](?=[^P]))|(W(?=[^MP]))', 'chymotrypsin low specificity': r'([FLY](?=[^P]))|(W(?=[^MP]))|(M(?=[^PY]))|(H(?=[^DMPW]))', 'clostripain': r'R', 'cnbr': r'M', 'enterokinase': r'(?<=[DE]{3})K', 'factor xa': r'(?<=[AFGILTVM][DE]G)R', 'formic acid': r'D', 'glutamyl endopeptidase': r'E', 'granzyme b': r'(?<=IEP)D', 'hydroxylamine': r'N(?=G)', 'iodosobenzoic acid': r'W', 'lysc': r'K', 'ntcb': r'\w(?=C)', 'pepsin ph1.3': r'((?<=[^HKR][^P])[^R](?=[FLWY][^P]))|' r'((?<=[^HKR][^P])[FLWY](?=\w[^P]))', 'pepsin ph2.0': r'((?<=[^HKR][^P])[^R](?=[FL][^P]))|' r'((?<=[^HKR][^P])[FL](?=\w[^P]))', 'proline endopeptidase': r'(?<=[HKR])P(?=[^P])', 'proteinase k': r'[AEFILTVWY]', 'staphylococcal peptidase i': r'(?<=[^E])E', 'thermolysin': r'[^DE](?=[AFILMV])', 'thrombin': r'((?<=G)R(?=G))|' r'((?<=[AFGILTVM][AFGILTVWA]P)R(?=[^DE][^DE]))', 'trypsin': r'([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=P))' } """ This dict contains regular expressions for cleavage rules of the most popular proteolytic enzymes. The rules were taken from the `PeptideCutter tool <http://ca.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html>`_ at Expasy. """