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annotate digest.py @ 0:038ecf54cbec draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219
author galaxyp
date Mon, 22 Jan 2018 13:59:27 -0500
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038ecf54cbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219
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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 itertools as it
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16 import re
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17 from collections import deque
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18
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19
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20 def cleave(sequence, rule, missed_cleavages=0, min_length=None):
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21 """Cleaves a polypeptide sequence using a given rule.
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22
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23 Parameters
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24 ----------
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25 sequence : str
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26 The sequence of a polypeptide.
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27
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28 .. note::
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29 The sequence is expected to be in one-letter uppercase notation.
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30 Otherwise, some of the cleavage rules in :py:data:`expasy_rules`
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31 will not work as expected.
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32
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33 rule : str or compiled regex
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34 A regular expression describing the site of cleavage. It is recommended
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35 to design the regex so that it matches only the residue whose
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36 C-terminal bond is to be cleaved. All additional requirements should be
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37 specified using `lookaround assertions
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38 <http://www.regular-expressions.info/lookaround.html>`_.
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39 :py:data:`expasy_rules` contains cleavage rules
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40 for popular cleavage agents.
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41 missed_cleavages : int, optional
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42 Maximum number of allowed missed cleavages. Defaults to 0.
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43 min_length : int or None, optional
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44 Minimum peptide length. Defaults to :py:const:`None`.
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45
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46 ..note ::
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47 This checks for string length, which is only correct for one-letter
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48 notation and not for full *modX*. Use :py:func:`length` manually if
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49 you know what you are doing and apply :py:func:`cleave` to *modX*
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50 sequences.
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51
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52 Returns
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53 -------
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54 out : set
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55 A set of unique (!) peptides.
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56
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57 Examples
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58 --------
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59 >>> cleave('AKAKBK', expasy_rules['trypsin'], 0) == {'AK', 'BK'}
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60 True
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61 >>> cleave('GKGKYKCK', expasy_rules['trypsin'], 2) == \
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62 {'CK', 'GKYK', 'YKCK', 'GKGK', 'GKYKCK', 'GK', 'GKGKYK', 'YK'}
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63 True
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64
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65 """
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66 return set(_cleave(sequence, rule, missed_cleavages, min_length))
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67
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68
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69 def _cleave(sequence, rule, missed_cleavages=0, min_length=None):
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70 """Like :py:func:`cleave`, but the result is a list. Refer to
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71 :py:func:`cleave` for explanation of parameters.
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72 """
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73 peptides = []
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74 ml = missed_cleavages+2
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75 trange = range(ml)
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76 cleavage_sites = deque([0], maxlen=ml)
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77 cl = 1
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78 for i in it.chain([x.end() for x in re.finditer(rule, sequence)],
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79 [None]):
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80 cleavage_sites.append(i)
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81 if cl < ml:
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82 cl += 1
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83 for j in trange[:cl-1]:
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84 seq = sequence[cleavage_sites[j]:cleavage_sites[-1]]
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85 if seq:
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86 if min_length is None or len(seq) >= min_length:
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87 peptides.append(seq)
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88 return peptides
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89
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90
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91 def num_sites(sequence, rule, **kwargs):
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92 """Count the number of sites where `sequence` can be cleaved using
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93 the given `rule` (e.g. number of miscleavages for a peptide).
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94
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95 Parameters
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96 ----------
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97 sequence : str
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98 The sequence of a polypeptide.
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99 rule : str or compiled regex
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100 A regular expression describing the site of cleavage. It is recommended
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101 to design the regex so that it matches only the residue whose
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102 C-terminal bond is to be cleaved. All additional requirements should be
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103 specified using `lookaround assertions
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104 <http://www.regular-expressions.info/lookaround.html>`_.
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105 labels : list, optional
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106 A list of allowed labels for amino acids and terminal modifications.
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107
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108 Returns
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109 -------
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110 out : int
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111 Number of cleavage sites.
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112 """
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113 return len(_cleave(sequence, rule, **kwargs)) - 1
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114
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115
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116 expasy_rules = {
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117 'arg-c': r'R',
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118 'asp-n': r'\w(?=D)',
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119 'bnps-skatole': r'W',
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120 'caspase 1': r'(?<=[FWYL]\w[HAT])D(?=[^PEDQKR])',
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121 'caspase 2': r'(?<=DVA)D(?=[^PEDQKR])',
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122 'caspase 3': r'(?<=DMQ)D(?=[^PEDQKR])',
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123 'caspase 4': r'(?<=LEV)D(?=[^PEDQKR])',
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124 'caspase 5': r'(?<=[LW]EH)D',
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125 'caspase 6': r'(?<=VE[HI])D(?=[^PEDQKR])',
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126 'caspase 7': r'(?<=DEV)D(?=[^PEDQKR])',
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127 'caspase 8': r'(?<=[IL]ET)D(?=[^PEDQKR])',
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128 'caspase 9': r'(?<=LEH)D',
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129 'caspase 10': r'(?<=IEA)D',
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130 'chymotrypsin high specificity': r'([FY](?=[^P]))|(W(?=[^MP]))',
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131 'chymotrypsin low specificity':
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132 r'([FLY](?=[^P]))|(W(?=[^MP]))|(M(?=[^PY]))|(H(?=[^DMPW]))',
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133 'clostripain': r'R',
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134 'cnbr': r'M',
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135 'enterokinase': r'(?<=[DE]{3})K',
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136 'factor xa': r'(?<=[AFGILTVM][DE]G)R',
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137 'formic acid': r'D',
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138 'glutamyl endopeptidase': r'E',
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139 'granzyme b': r'(?<=IEP)D',
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140 'hydroxylamine': r'N(?=G)',
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141 'iodosobenzoic acid': r'W',
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142 'lysc': r'K',
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143 'ntcb': r'\w(?=C)',
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144 'pepsin ph1.3': r'((?<=[^HKR][^P])[^R](?=[FLWY][^P]))|'
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145 r'((?<=[^HKR][^P])[FLWY](?=\w[^P]))',
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146 'pepsin ph2.0': r'((?<=[^HKR][^P])[^R](?=[FL][^P]))|'
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147 r'((?<=[^HKR][^P])[FL](?=\w[^P]))',
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148 'proline endopeptidase': r'(?<=[HKR])P(?=[^P])',
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149 'proteinase k': r'[AEFILTVWY]',
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150 'staphylococcal peptidase i': r'(?<=[^E])E',
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151 'thermolysin': r'[^DE](?=[AFILMV])',
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152 'thrombin': r'((?<=G)R(?=G))|'
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153 r'((?<=[AFGILTVM][AFGILTVWA]P)R(?=[^DE][^DE]))',
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154 'trypsin': r'([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=P))'
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155 }
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156 """
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157 This dict contains regular expressions for cleavage rules of the most
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158 popular proteolytic enzymes. The rules were taken from the
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159 `PeptideCutter tool
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160 <http://ca.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html>`_
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161 at Expasy.
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162 """