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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 from commons.core.writer.TranscriptListWriter import TranscriptListWriter
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31
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32
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33 class BedWriter(TranscriptListWriter):
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34 """
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35 A class that writes a transcript list into a file with BED format
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36 @ivar fileName: name of the file
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37 @type fileName: string
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38 @ivar handle: handle to the file
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39 @type handle: file handle
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40 @ivar header: first lines of the file
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41 @type header: string
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42 """
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43
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44
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45 def __init__(self, fileName, verbosity = 0):
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46 """
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47 Constructor
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48 @param fileName: name of the file
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49 @type fileName: string
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50 @param verbosity: verbosity
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51 @type verbosity: int
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52 """
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53 self.header = "track name=reads description=\"Reads\" useScore=0 visibility=full offset=0\n"
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54 super(BedWriter, self).__init__(fileName, verbosity)
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55
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56
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57 @staticmethod
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58 def getFileFormats():
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59 """
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60 Get the format of the file
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61 """
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62 return ["bed"]
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63
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64
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65 @staticmethod
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66 def getExtension():
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67 """
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68 Get the usual extension for the file
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69 """
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70 return "bed"
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71
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72
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73 def setTitle(self, title):
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74 """
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75 Set the title of the track
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76 @param title: the title of the track
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77 @type title: string
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78 """
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79 if title != None:
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80 self.header = "track name=%s description=\"%s\" useScore=0 visibility=full offset=0\n" % (title, title)
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81
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82
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83 def copyProperties(self, bedParser):
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84 """
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85 Copy the properties collected by a parser, to produce a similar output
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86 @param bedParser: a BED Parser parser
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87 @type bedParser: class L{BedParser<BedParser>}
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88 """
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89 self.setTitle(bedParser.title)
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90
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91
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92 def printTranscript(self, transcript):
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93 """
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94 Export the given transcript with GBrowse format
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95 @param transcript: transcript to be printed
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96 @type transcript: class L{Transcript<Transcript>}
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97 @return: a string
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98 """
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99 return transcript.printBed()
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100
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