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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 os
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31 import random
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32 from commons.core.writer.TranscriptListWriter import TranscriptListWriter
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33 from SMART.Java.Python.misc.Progress import Progress
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34
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35 class CsvWriter(TranscriptListWriter):
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36 """
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37 A class that writes a transcript list into a file with CSV (Excel) format
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38 @ivar fileName: name of the file
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39 @type fileName: string
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40 @ivar handle: handle to the file
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41 @type handle: file handle
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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 super(CsvWriter, self).__init__(fileName, verbosity)
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54 self.header = ""
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55 self.title = "chromosome,start,end,strand,exons,tags\n"
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56 self.modified = False
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57
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58
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59 def __del__(self):
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60 """
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61 Destructor
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62 (Trick to write 1 tag per column)
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63 """
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64 if self.handle != None:
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65 self.modifyCsv()
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66 super(CsvWriter, self).__del__()
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67
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68
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69 def close(self):
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70 if self.handle != None:
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71 self.modifyCsv()
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72 super(CsvWriter, self).close()
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73
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74
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75 def modifyCsv(self):
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76 """
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77 Clean CSV file so that there is one column per tag
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78 """
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79 if self.modified:
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80 return
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81
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82 # read all the tags
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83 self.handle.close()
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84 self.handle = open(self.fileName)
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85 nbFirstFields = 5
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86 tags = set()
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87 if self.verbosity >= 10:
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88 print "Modifying CSV file..."
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89 number = -1
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90 for number, line in enumerate(self.handle):
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91 if number != 0:
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92 theseTags = line.strip().split(",")[nbFirstFields:]
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93 for tag in theseTags:
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94 if tag.find("=") != -1:
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95 (key, value) = tag.split("=", 1)
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96 if value != None:
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97 tags.add(key)
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98 if self.verbosity >= 10:
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99 print " ...done"
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100
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101 # re-write the file
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102 tmpFileName = "tmpFile%d.csv" % (random.randint(0, 100000))
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103 tmpFile = open(tmpFileName, "w")
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104 self.handle.seek(0)
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105 progress = Progress(number + 1, "Re-writting CSV file", self.verbosity)
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106 tmpFile.write(self.title.replace("tags", ",".join(sorted(tags))))
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107 for line in self.handle:
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108 tagValues = dict([(key, None) for key in tags])
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109 tmpFile.write(",".join(line.strip().split(",")[:nbFirstFields]))
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110 for tag in line.strip().split(",")[nbFirstFields:]:
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111 if tag.find("=") != -1:
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112 key = tag.split("=", 1)[0]
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113 tagValues[key] = tag.split("=", 1)[1]
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114 else:
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115 tagValues[key] += ";%s" % (tag)
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116 for key in sorted(tagValues.keys()):
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117 tmpFile.write(",%s" % (tagValues[key]))
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118 tmpFile.write("\n")
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119 progress.inc()
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120 tmpFile.close()
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121
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122 # replace former file
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123 import shutil
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124 shutil.move(tmpFile.name, self.fileName)
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125 progress.done()
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126 self.modified = True
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127
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128
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129 @staticmethod
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130 def getFileFormats():
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131 """
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132 Get the format of the file
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133 """
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134 return ["csv", "xls", "excel"]
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135
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136
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137 @staticmethod
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138 def getExtension():
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139 """
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140 Get the usual extension for the file
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141 """
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142 return "csv"
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143
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144
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145 def printTranscript(self, transcript):
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146 """
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147 Export the given transcript with GFF2 format
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148 @param transcript: transcript to be printed
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149 @type transcript: class L{Transcript<Transcript>}
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150 @return: a string
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151 """
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152 return transcript.printCsv()
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153
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