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6
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1 #
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2 # Copyright INRA-URGI 2009-2010
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3 #
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4 # This software is governed by the CeCILL license under French law and
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5 # abiding by the rules of distribution of free software. You can use,
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6 # modify and/ or redistribute the software under the terms of the CeCILL
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
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8 # "http://www.cecill.info".
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9 #
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10 # As a counterpart to the access to the source code and rights to copy,
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11 # modify and redistribute granted by the license, users are provided only
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12 # with a limited warranty and the software's author, the holder of the
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13 # economic rights, and the successive licensors have only limited
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14 # liability.
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15 #
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16 # In this respect, the user's attention is drawn to the risks associated
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17 # with loading, using, modifying and/or developing or reproducing the
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18 # software by the user in light of its specific status of free software,
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19 # that may mean that it is complicated to manipulate, and that also
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20 # therefore means that it is reserved for developers and experienced
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21 # professionals having in-depth computer knowledge. Users are therefore
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22 # encouraged to load and test the software's suitability as regards their
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23 # requirements in conditions enabling the security of their systems and/or
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24 # data to be ensured and, more generally, to use and operate it in the
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25 # same conditions as regards security.
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26 #
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27 # The fact that you are presently reading this means that you have had
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28 # knowledge of the CeCILL license and that you accept its terms.
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29 #
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30 import math
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31
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32 class SequenceList(object):
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33 """A class that codes for a list of sequences"""
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34
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35 def __init__(self, verbosity = 0):
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36 self.sequences = []
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37 self.verbosity = verbosity
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38
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39
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40 def nbSequences(self):
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41 return len(self.sequences)
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42
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43
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44 def getSequence(self, index):
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45 return self.sequences[index]
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46
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47
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48 def addSequence(self, sequence):
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49 self.sequences.append(sequence)
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50
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51
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52 def split(self, number):
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53 sequenceLists = []
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54 size = math.ceil(self.nbSequences() / number)
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55
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56 sequenceList = SequenceList()
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57 for i in range(0, self.nbSequences()):
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58 sequenceList.addSequence(self.getSequence(i))
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59 if (sequenceList.nbSequences() == size):
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60 sequenceLists.append(sequenceList)
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61 sequenceList = SequenceList()
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62 if (sequenceList.nbSequences() != 0):
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63 sequenceLists.append(sequenceList)
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64 return sequenceLists
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65
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66
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67 def printFasta(self):
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68 string = ""
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69 for sequence in self.sequences:
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70 string += sequence.printFasta()
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71 return string
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72
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