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1 # Copyright 2012 Anton Goloborodko, Lev Levitsky
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2 #
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3 # Licensed under the Apache License, Version 2.0 (the "License");
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4 # you may not use this file except in compliance with the License.
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5 # You may obtain a copy of the License at
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6 #
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7 # http://www.apache.org/licenses/LICENSE-2.0
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8 #
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9 # Unless required by applicable law or agreed to in writing, software
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10 # distributed under the License is distributed on an "AS IS" BASIS,
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11 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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12 # See the License for the specific language governing permissions and
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13 # limitations under the License.
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14
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15 import re
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16 from collections import deque
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17 import itertools as it
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18
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19 def cleave(sequence, rule, missed_cleavages=0, min_length=None):
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20 """Cleaves a polypeptide sequence using a given rule.
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21
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22 Parameters
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23 ----------
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24 sequence : str
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25 The sequence of a polypeptide.
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26
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27 .. note::
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28 The sequence is expected to be in one-letter uppercase notation.
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29 Otherwise, some of the cleavage rules in :py:data:`expasy_rules`
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30 will not work as expected.
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31
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32 rule : str or compiled regex
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33 A regular expression describing the site of cleavage. It is recommended
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34 to design the regex so that it matches only the residue whose C-terminal
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35 bond is to be cleaved. All additional requirements should be specified
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36 using `lookaround assertions
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37 <http://www.regular-expressions.info/lookaround.html>`_.
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38 :py:data:`expasy_rules` contains cleavage rules for popular cleavage agents.
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39 missed_cleavages : int, optional
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40 Maximum number of allowed missed cleavages. Defaults to 0.
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41 min_length : int or None, optional
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42 Minimum peptide length. Defaults to :py:const:`None`.
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43
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44 ..note ::
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45 This checks for string length, which is only correct for one-letter
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46 notation and not for full *modX*. Use :py:func:`length` manually if
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47 you know what you are doing and apply :py:func:`cleave` to *modX*
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48 sequences.
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49
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50 Returns
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51 -------
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52 out : set
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53 A set of unique (!) peptides.
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54
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55 Examples
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56 --------
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57 >>> cleave('AKAKBK', expasy_rules['trypsin'], 0) == {'AK', 'BK'}
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58 True
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59 >>> cleave('GKGKYKCK', expasy_rules['trypsin'], 2) == \
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60 {'CK', 'GKYK', 'YKCK', 'GKGK', 'GKYKCK', 'GK', 'GKGKYK', 'YK'}
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61 True
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62
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63 """
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64 return set(_cleave(sequence, rule, missed_cleavages, min_length))
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65
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66 def _cleave(sequence, rule, missed_cleavages=0, min_length=None):
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67 """Like :py:func:`cleave`, but the result is a list. Refer to
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68 :py:func:`cleave` for explanation of parameters.
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69 """
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70 peptides = []
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71 ml = missed_cleavages+2
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72 trange = range(ml)
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73 cleavage_sites = deque([0], maxlen=ml)
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74 cl = 1
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75 for i in it.chain([x.end() for x in re.finditer(rule, sequence)],
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76 [None]):
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77 cleavage_sites.append(i)
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78 if cl < ml:
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79 cl += 1
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80 for j in trange[:cl-1]:
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81 seq = sequence[cleavage_sites[j]:cleavage_sites[-1]]
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82 if seq:
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83 if min_length is None or len(seq) >= min_length:
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84 peptides.append(seq)
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85 return peptides
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86
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87 def num_sites(sequence, rule, **kwargs):
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88 """Count the number of sites where `sequence` can be cleaved using
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89 the given `rule` (e.g. number of miscleavages for a peptide).
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90
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91 Parameters
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92 ----------
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93 sequence : str
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94 The sequence of a polypeptide.
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95 rule : str or compiled regex
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96 A regular expression describing the site of cleavage. It is recommended
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97 to design the regex so that it matches only the residue whose C-terminal
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98 bond is to be cleaved. All additional requirements should be specified
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99 using `lookaround assertions
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100 <http://www.regular-expressions.info/lookaround.html>`_.
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101 labels : list, optional
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102 A list of allowed labels for amino acids and terminal modifications.
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103
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104 Returns
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105 -------
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106 out : int
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107 Number of cleavage sites.
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108 """
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109 return len(_cleave(sequence, rule, **kwargs)) - 1
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110
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111 expasy_rules = {
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112 'arg-c': r'R',
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113 'asp-n': r'\w(?=D)',
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114 'bnps-skatole' : r'W',
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115 'caspase 1': r'(?<=[FWYL]\w[HAT])D(?=[^PEDQKR])',
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116 'caspase 2': r'(?<=DVA)D(?=[^PEDQKR])',
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117 'caspase 3': r'(?<=DMQ)D(?=[^PEDQKR])',
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118 'caspase 4': r'(?<=LEV)D(?=[^PEDQKR])',
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119 'caspase 5': r'(?<=[LW]EH)D',
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120 'caspase 6': r'(?<=VE[HI])D(?=[^PEDQKR])',
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121 'caspase 7': r'(?<=DEV)D(?=[^PEDQKR])',
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122 'caspase 8': r'(?<=[IL]ET)D(?=[^PEDQKR])',
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123 'caspase 9': r'(?<=LEH)D',
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124 'caspase 10': r'(?<=IEA)D',
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125 'chymotrypsin high specificity' : r'([FY](?=[^P]))|(W(?=[^MP]))',
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126 'chymotrypsin low specificity':
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127 r'([FLY](?=[^P]))|(W(?=[^MP]))|(M(?=[^PY]))|(H(?=[^DMPW]))',
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128 'clostripain': r'R',
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129 'cnbr': r'M',
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130 'enterokinase': r'(?<=[DE]{3})K',
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131 'factor xa': r'(?<=[AFGILTVM][DE]G)R',
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132 'formic acid': r'D',
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133 'glutamyl endopeptidase': r'E',
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134 'granzyme b': r'(?<=IEP)D',
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135 'hydroxylamine': r'N(?=G)',
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136 'iodosobenzoic acid': r'W',
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137 'lysc': r'K',
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138 'ntcb': r'\w(?=C)',
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139 'pepsin ph1.3': r'((?<=[^HKR][^P])[^R](?=[FLWY][^P]))|'
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140 r'((?<=[^HKR][^P])[FLWY](?=\w[^P]))',
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141 'pepsin ph2.0': r'((?<=[^HKR][^P])[^R](?=[FL][^P]))|'
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142 r'((?<=[^HKR][^P])[FL](?=\w[^P]))',
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143 'proline endopeptidase': r'(?<=[HKR])P(?=[^P])',
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144 'proteinase k': r'[AEFILTVWY]',
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145 'staphylococcal peptidase i': r'(?<=[^E])E',
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146 'thermolysin': r'[^DE](?=[AFILMV])',
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147 'thrombin': r'((?<=G)R(?=G))|'
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148 r'((?<=[AFGILTVM][AFGILTVWA]P)R(?=[^DE][^DE]))',
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149 'trypsin': r'([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=P))'
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150 }
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151 """
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152 This dict contains regular expressions for cleavage rules of the most
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153 popular proteolytic enzymes. The rules were taken from the
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154 `PeptideCutter tool
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155 <http://ca.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html>`_
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156 at Expasy.
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157 """
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158
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