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2 # Copyright (c) 2006 John Gilman
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3 #
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4 # This software is distributed under the MIT Open Source License.
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5 # <http://www.opensource.org/licenses/mit-license.html>
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6 #
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7 # Permission is hereby granted, free of charge, to any person obtaining a
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8 # copy of this software and associated documentation files (the "Software"),
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9 # to deal in the Software without restriction, including without limitation
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10 # the rights to use, copy, modify, merge, publish, distribute, sublicense,
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11 # and/or sell copies of the Software, and to permit persons to whom the
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12 # Software is furnished to do so, subject to the following conditions:
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13 #
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14 # The above copyright notice and this permission notice shall be included
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15 # in all copies or substantial portions of the Software.
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16 #
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17 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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18 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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19 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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20 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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21 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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22 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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23 # THE SOFTWARE.
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24
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25
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26 """Read BLAST XML output.
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27
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28 The DTD is available at
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29 http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd
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30
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31 """
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32
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33 # See also
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34 #
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35 # http://bugzilla.open-bio.org/show_bug.cgi?id=1933
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36 #http://portal.open-bio.org/pipermail/biojava-dev/2004-December/002513.html
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37
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38
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39 from corebio.ssearch_io import Report, Result, Hit, Annotation, Alignment
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40
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41 import xml.sax
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42 from xml.sax.handler import ContentHandler
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43
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44 __all__ = 'read'
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45
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46 def read(fin):
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47 """Read BLAST xml output and return a list of Result objects.
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48 """
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49 parser = xml.sax.make_parser()
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50 handler = _BlastHandler()
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51 parser.setContentHandler(handler)
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52
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53 #To avoid ValueError: unknown url type: NCBI_BlastOutput.dtd
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54 parser.setFeature(xml.sax.handler.feature_validation, 0)
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55 parser.setFeature(xml.sax.handler.feature_namespaces, 0)
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56 parser.setFeature(xml.sax.handler.feature_external_pes, 0)
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57 parser.setFeature(xml.sax.handler.feature_external_ges, 0)
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58
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59 try :
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60 parser.parse(fin)
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61 except xml.sax.SAXParseException, e :
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62 raise ValueError( "Cannot parse file; "+str(e))
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63 return handler.report
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64
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65 class _BlastHandler( ContentHandler) :
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66 def __init__(self):
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67 """
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68 """
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69 ContentHandler.__init__(self)
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70 self._content = []
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71 self.report = None
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72 self._result = None
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73 self._hit = None
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74 self._hsp = None
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75
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76
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77 def characters(self, ch):
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78 self._content.append(ch)
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79
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80 def startDocument(self):
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81 self.report = Report()
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82
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83 def endDocument(self) :
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84 pass
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85
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86 def startElement(self, name, attr):
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87 if name == 'BlastOutput' :
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88 pass
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89 elif name == 'Iteration' :
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90 result = Result()
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91 self._result = result
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92 self.report.results.append(result)
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93 elif name == 'Parameters' :
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94 pass
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95 elif name == 'Statistics' :
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96 pass
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97 elif name == 'Hit' :
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98 self._hit = Hit()
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99 self._result.hits.append(self._hit)
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100 elif name == 'Hsp' :
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101 self._hsp = Alignment()
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102 self._hit.alignments.append(self._hsp)
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103 else :
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104 pass
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105
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106
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107 def endElement(self, name):
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108 content = ''.join(self._content).strip()
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109 self._content = []
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110
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111 report = self.report
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112 result = self._result
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113 hsp = self._hsp
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114 hit = self._hit
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115
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116 if name == 'BlastOutput' :
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117 pass
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118 elif name == 'BlastOutput_program' :
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119 report.algorithm = content
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120 elif name == 'BlastOutput_version' :
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121 report.algorithm_version = content.split()[1]
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122 elif name == 'BlastOutput_reference' :
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123 report.algorithm_reference = content
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124 elif name == 'BlastOutput_db' :
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125 report.database_name = content
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126 elif name == 'BlastOutput_query-ID' : pass
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127 elif name == 'BlastOutput_query-def' : pass
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128 elif name == 'BlastOutput_query-len' : pass
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129 elif name == 'BlastOutput_query-seq' : pass
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130 elif name == 'BlastOutput_param' : pass
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131 elif name == 'BlastOutput_iterations' : pass
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132 elif name == 'BlastOutput_mbstat' : pass
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133
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134 elif name == 'Iteration' : pass
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135 elif name == 'Iteration_iter-num' : pass
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136 elif name == 'Iteration_query-ID' :
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137 result.query.name = content
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138 elif name == 'Iteration_query-def' :
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139 result.query.description = content
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140 elif name == 'Iteration_query-len' :
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141 result.query.length = int(content)
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142 elif name == 'Iteration_hits' : pass
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143 elif name == 'Iteration_stat' : pass
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144 elif name == 'Iteration_message' : pass
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145
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146 elif name == 'Parameters' :
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147 pass
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148 elif name == 'Parameters_matrix' :
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149 report.parameters['matrix'] = content
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150 elif name == 'Parameters_expect' :
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151 report.parameters['expect'] = content
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152 elif name == 'Parameters_include' :
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153 report.parameters['include'] = content
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154 elif name == 'Parameters_sc-match' :
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155 report.parameters['sc-match'] = content
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156 elif name == 'Parameters_sc-mismatch' :
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157 report.parameters['sc-mismatch'] = content
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158 elif name == 'Parameters_gap-open' :
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159 report.parameters['gap-open'] = content
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160 elif name == 'Parameters_gap-extend' :
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161 report.parameters['gap-extend'] = content
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162 elif name == 'Parameters_filter' :
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163 report.parameters['filter'] = content
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164 elif name == 'Parameters_pattern' :
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165 report.parameters['pattern'] = content
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166 elif name == 'Parameters_entrez-query' :
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167 report.parameters['entrez-query'] = content
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168
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169 elif name == 'Statistics' :
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170 pass
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171 elif name == 'Statistics_db-num' :
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172 result.statistics['db-num'] = int(content)
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173 elif name == 'Statistics_db-len' :
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174 result.statistics['db-len'] = int(content)
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175 elif name == 'Statistics_hsp-len' :
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176 result.statistics['hsp-len'] = int(content)
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177 elif name == 'Statistics_eff-space' :
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178 result.statistics['eff-space'] = float(content)
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179 elif name == 'Statistics_kappa' :
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180 result.statistics['kappa'] = float(content)
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181 elif name == 'Statistics_lambda' :
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182 result.statistics['lambda'] = float(content)
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183 elif name == 'Statistics_entropy' :
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184 result.statistics['entropy'] = float(content)
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185
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186 elif name == 'Hit' :
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187 self._hit = None
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188 elif name == 'Hit_num' :
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189 pass
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190 elif name == 'Hit_id' :
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191 hit.target.name = content
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192 elif name == 'Hit_def' :
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193 hit.target.description = content
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194 elif name == 'Hit_accession' :
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195 hit.target.accession = content
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196 elif name == 'Hit_len' :
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197 hit.target.length = int(content)
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198 elif name == 'Hit_hsps' :
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199 pass
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200
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201 elif name == 'Hsp' :
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202 self._hsp = None
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203 elif name == 'Hsp_num' :
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204 pass
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205 elif name == 'Hsp_bit-score' :
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206 hsp.bit_score = float(content)
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207 elif name == 'Hsp_score' :
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208 hsp.raw_score = float(content)
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209 elif name == 'Hsp_evalue' :
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210 hsp.significance = float(content)
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211 elif name == 'Hsp_query-from' :
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212 hsp.query_start = int(content) -1
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213 elif name == 'Hsp_query-to' :
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214 #hsp.query_end= int(content)
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215 pass
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216 elif name == 'Hsp_hit-from' :
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217 hsp.target_start = int(content) -1
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218 elif name == 'Hsp_hit-to' :
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219 #hsp.target_end = int(content)
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220 pass
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221 elif name == 'Hsp_pattern-from' :
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222 pass
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223 elif name == 'Hsp_pattern-to' :
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224 pass
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225 elif name == 'Hsp_query-frame' :
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226 hsp.query_frame = int(content)
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227 elif name == 'Hsp_hit-frame' :
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228 hsp.target_frame = int(content)
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229 elif name == 'Hsp_identity' :
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230 hsp.identical = int(content)
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231 elif name == 'Hsp_positive' :
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232 hsp.similar = int(content)
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233 elif name == 'Hsp_gaps' :
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234 hsp.gaps = int(content)
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235 elif name == 'Hsp_align-len' :
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236 hsp.length = int(content)
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237 elif name == 'Hsp_density' :
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238 pass
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239 elif name == 'Hsp_qseq' :
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240 hsp.query_seq = content
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241 elif name == 'Hsp_hseq' :
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242 hsp.target_seq = content
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243 elif name == 'Hsp_midline' :
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244 hsp.mid_seq = content
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245 else :
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246 pass
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247
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248
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249
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