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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 WigWriter(TranscriptListWriter):
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34 """
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35 A class that writes a transcript list into a file with WIGGLE 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.fileName = fileName
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54 self.verbosity = verbosity
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55 self.data = {-1: {}, 0: {}, 1: {}}
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56 self.title = "Reads"
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57 self.strands = False
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58 self.handle = None
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59
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60
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61 def __del__(self):
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62 """
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63 Destructor
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64 Actually print the file
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65 """
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66 strand2string = {-1: "-", 1: "+", 0: ""}
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67 self.handle = open(self.fileName, "w")
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68 self.handle.write("track type=wiggle_0 name=\"%s\"\n" % (self.title))
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69 for strand in self.data:
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70 for chromosome in sorted(self.data[strand]):
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71 self.handle.write("variableStep chrom=%s%s\n" % (chromosome, strand2string[strand]))
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72 for pos in sorted(self.data[strand][chromosome]):
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73 self.handle.write("%d\t%d\n" % (pos, self.data[strand][chromosome][pos]))
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74 self.handle.close()
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75
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76
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77 @staticmethod
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78 def getFileFormats():
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79 """
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80 Get the format of the file
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81 """
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82 return ["wig", "wiggle"]
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83
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84
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85 @staticmethod
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86 def getExtension():
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87 """
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88 Get the usual extension for the file
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89 """
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90 return "wig"
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91
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92
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93 def setTitle(self, title):
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94 """
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95 Set the title of the track
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96 @param title: the title of the track
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97 @type title: string
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98 """
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99 if title != None:
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100 self.title = title
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101
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102
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103 def setStrands(self, strands):
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104 """
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105 Consider each strand separately
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106 @param boolean: whether each strand should be considered separately
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107 @type boolean: boolean
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108 """
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109 self.strands = strands
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110
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111
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112 def copyProperties(self, parser):
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113 """
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114 Copy the properties collected by a parser, to produce a similar output
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115 @param bedParser: a parser
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116 @type bedParser: class L{TranscriptListWriter<TranscriptListWriter>}
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117 """
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118 self.setTitle(parser.title)
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119
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120
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121 def addTranscript(self, transcript):
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122 """
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123 Export the given transcript with GBrowse format
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124 @param transcript: transcript to be printed
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125 @type transcript: class L{Transcript<Transcript>}
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126 @return: a string
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127 """
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128 chromosome = transcript.getChromosome()
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129 direction = transcript.getDirection()
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130 if not self.strands:
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131 direction = 0
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132 if chromosome not in self.data[direction]:
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133 self.data[direction][chromosome] = {}
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134 for exon in transcript.getExons():
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135 for pos in range(exon.getStart(), exon.getEnd()+1):
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136 if pos not in self.data[direction][chromosome]:
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137 self.data[direction][chromosome][pos] = 1
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138 else:
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139 self.data[direction][chromosome][pos] += 1
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