Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/structure/Sequence.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 #
2 # Copyright INRA-URGI 2009-2010
3 #
4 # This software is governed by the CeCILL license under French law and
5 # abiding by the rules of distribution of free software. You can use,
6 # modify and/ or redistribute the software under the terms of the CeCILL
7 # license as circulated by CEA, CNRS and INRIA at the following URL
8 # "http://www.cecill.info".
9 #
10 # As a counterpart to the access to the source code and rights to copy,
11 # modify and redistribute granted by the license, users are provided only
12 # with a limited warranty and the software's author, the holder of the
13 # economic rights, and the successive licensors have only limited
14 # liability.
15 #
16 # In this respect, the user's attention is drawn to the risks associated
17 # with loading, using, modifying and/or developing or reproducing the
18 # software by the user in light of its specific status of free software,
19 # that may mean that it is complicated to manipulate, and that also
20 # therefore means that it is reserved for developers and experienced
21 # professionals having in-depth computer knowledge. Users are therefore
22 # encouraged to load and test the software's suitability as regards their
23 # requirements in conditions enabling the security of their systems and/or
24 # data to be ensured and, more generally, to use and operate it in the
25 # same conditions as regards security.
26 #
27 # The fact that you are presently reading this means that you have had
28 # knowledge of the CeCILL license and that you accept its terms.
29 #
30 import sys
31 import re
32 from commons.core.seq.Bioseq import Bioseq
33
34 reverseComplementString = {
35 "A": "T",
36 "C": "G",
37 "G": "C",
38 "T": "A",
39 "U": "A",
40 "M": "K",
41 "R": "Y",
42 "W": "W",
43 "S": "S",
44 "Y": "R",
45 "K": "M",
46 "V": "B",
47 "H": "D",
48 "D": "H",
49 "B": "V",
50 "N": "N",
51 "a": "t",
52 "c": "g",
53 "g": "c",
54 "t": "a",
55 "u": "a",
56 "m": "k",
57 "r": "y",
58 "w": "w",
59 "s": "s",
60 "y": "r",
61 "k": "m",
62 "v": "b",
63 "h": "d",
64 "d": "h",
65 "b": "v",
66 "n": "n"
67 }
68
69 class Sequence(Bioseq):
70 """A class that codes for a sequence"""
71
72 def __init__(self, name = "", sequence = ""):
73 super(Sequence, self).__init__(name, sequence)
74 self.name = self.header
75 self.quality = None
76 self.chunkedSequence = None
77 self.chunkedQuality = None
78 self.integerQuality = False
79
80 def setName(self, name=""):
81 super(Sequence, self).setHeader(name)
82
83 def getName(self):
84 return self.getHeader()
85
86 def setSequence(self, seq=""):
87 super(Sequence, self).setSequence(seq)
88
89 def setQuality(self, quality):
90 if quality == None:
91 self.quality = None
92 return
93 if " " in quality:
94 self.quality = quality.split()
95 self.integerQuality = True
96 else:
97 self.quality = list(quality)
98
99 def getQuality(self):
100 if self.quality == None:
101 return None
102 if self.integerQuality:
103 return " ".join(self.quality)
104 return "".join(self.quality)
105
106 def getSize(self):
107 return len(self.getSequence())
108
109
110 def copy(self, sequence):
111 self.setName(sequence.getName())
112 self.setSequence(sequence.getSequence())
113 self.setQuality(sequence.getQuality())
114 self.chunkedSequence = None
115 self.chunkedQuality = None
116
117
118 def chunkSequence(self):
119 self.chunkedSequence = []
120 for i in range (0, self.getSize() / 60 + 1):
121 self.chunkedSequence.append(self.getSequence()[i * 60 : min(self.getSize(), (i+1) * 60)])
122 if self.quality != None:
123 self.chunkedQuality = []
124 for i in range (0, self.getSize() / 60 + 1):
125 self.chunkedQuality.append(self.quality[i * 60 : min(self.getSize(), (i+1) * 60)])
126
127 def concatenate(self, seq):
128 sequence = self.getSequence()
129 sequence += seq.getSequence()
130 self.setSequence(sequence)
131 if self.quality != None:
132 sep = " " if self.integerQuality else ""
133 self.setQuality(self.getQuality() + sep + seq.getQuality())
134 self.chunkedSequence = None
135 self.chunkedQuality = None
136
137
138 def printFasta(self):
139 if self.chunkedSequence == None:
140 self.chunkSequence()
141 return ">%s\n%s\n" % (self.getHeader(), "\n".join(self.chunkedSequence))
142
143
144 def printFastq(self):
145 if self.chunkedSequence == None:
146 self.chunkSequence()
147 return "@%s\n%s\n+%s\n%s\n" % (self.getHeader(), self.getSequence(), self.getHeader(), self.getQuality())
148
149
150 def reverseComplement(self):
151 seq = ""
152 self.chunkedSequence = None
153 self.chunkedQuality = None
154 for i in range(0, self.getSize()):
155 char = self.getSequence()[i:i+1]
156 if char not in reverseComplementString:
157 sys.exit("Cannot understand character %s from string %s" % (char, self.getSequence()))
158 seq = "%s%s" % (reverseComplementString[char], seq)
159 self.setSequence(seq)
160 if self.quality != None:
161 self.quality = self.quality[::-1]
162
163
164 def containsAmbiguousNucleotides(self):
165 m = re.search("[^ACGTUacgtu]", self.getSequence())
166 if m != None:
167 return True
168 return False
169
170
171 def shrinkToFirstNucleotides(self, nbNucleotides):
172 self.chunkedSequence = None
173 self.chunkedQuality = None
174 self.setSequence(self.getSequence()[0:nbNucleotides])
175 if self.quality != None:
176 self.quality = self.quality[0:nbNucleotides]
177
178
179 def shrinkToLastNucleotides(self, nbNucleotides):
180 self.chunkedSequence = None
181 self.chunkedQuality = None
182 self.setSequence(self.getSequence()[-nbNucleotides:])
183 if self.quality != None:
184 self.quality = self.quality[-nbNucleotides:]