Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/Java/Python/structure/SequenceList.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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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 math | |
31 | |
32 class SequenceList(object): | |
33 """A class that codes for a list of sequences""" | |
34 | |
35 def __init__(self, verbosity = 0): | |
36 self.sequences = [] | |
37 self.verbosity = verbosity | |
38 | |
39 | |
40 def nbSequences(self): | |
41 return len(self.sequences) | |
42 | |
43 | |
44 def getSequence(self, index): | |
45 return self.sequences[index] | |
46 | |
47 | |
48 def addSequence(self, sequence): | |
49 self.sequences.append(sequence) | |
50 | |
51 | |
52 def split(self, number): | |
53 sequenceLists = [] | |
54 size = math.ceil(self.nbSequences() / number) | |
55 | |
56 sequenceList = SequenceList() | |
57 for i in range(0, self.nbSequences()): | |
58 sequenceList.addSequence(self.getSequence(i)) | |
59 if (sequenceList.nbSequences() == size): | |
60 sequenceLists.append(sequenceList) | |
61 sequenceList = SequenceList() | |
62 if (sequenceList.nbSequences() != 0): | |
63 sequenceLists.append(sequenceList) | |
64 return sequenceLists | |
65 | |
66 | |
67 def printFasta(self): | |
68 string = "" | |
69 for sequence in self.sequences: | |
70 string += sequence.printFasta() | |
71 return string | |
72 |