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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 """ Parse the output of BLAST and similar sequence search analysis reports.
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26
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27 The result of a sequence database search is represented by the Report class.
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28 o Each Report contains one or more results, one for each database query.
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29 o Each Result contains one or more hits
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30 o Each Hit may contain one or more Alignments (High scoring Sequence pairs)
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31
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32 CoreBio is often capable of guessing the correct format:
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33 >>> from corebio import ssearch_io
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34 >>> afile = open("test_corebio/data/ssearch/ssearch_out.txt")
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35 >>> report = ssearch_io.read(afile)
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36 >>> print report
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37
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38 Alternatively, each report type has a seperate module. Each module defines a
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39 read(fin) method that can parse that report format.
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40
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41 >>> from corebio.ssearch_io import fasta
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42 >>> report = fasta.read( open("test_corebio/data/ssearch/ssearch_out.txt") )
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43 >>> print report
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44
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45 Module Application Comments
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46 ---------------------------------------------------------------------------
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47 fasta FASTA / SSEARCH Default (-m 1) or compact (-m 9 -d 0)
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48 blastxml NCBI Blast NCBI XML format
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49
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50 Status: Beta
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51 """
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52 # Dev. References :
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53 # Inspired by Bioperls searchIO system
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54 # http://www.bioperl.org/wiki/HOWTO:SearchIO
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55
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56 __all__ = ['read', 'Report', 'Result',
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57 'Hit','Annotation', 'Alignment']
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58
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59
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60 from corebio.utils import stdrepr
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61
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62 def read(fin) :
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63 """ Read and parse an analysis report.
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64
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65 returns :
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66 A database search Report.
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67 raises :
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68 ValueError - If the file cannot be parsed
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69 """
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70
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71 import fasta
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72 import blastxml
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73 parsers = (fasta, blastxml)
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74 for p in parsers:
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75 try:
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76 return p.read(fin)
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77 except ValueError, e:
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78 pass
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79 fin.seek(0) # FIXME. Non seakable stdin?
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80
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81 raise ValueError("Cannot parse sequence file: Tried fasta and blastxml")
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82
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83
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84
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85 class Report(object) :
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86 """The results of a database search. The Report contains a list of 1 or more
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87 Results, one for each query. Each query result containts a list of hits.
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88 Each Hit contains a list of HSP's (High scoring segment pairs).
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89
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90 The structure of the report will vary somewhat depending on the source.
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91
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92 algorithm -- e.g. 'BLASTX'
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93 algorithm_version -- e.g. '2.2.4 [Aug-26-2002]'
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94 algorithm_reference --
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95 database_name -- e.g. 'test.fa'
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96 database_letters -- number of residues in database e.g. 1291
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97 database_entries -- number of database entries
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98
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99 parameters -- Dictionary of parameters used in search
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100
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101 results -- A list of list of Results, one per query
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102 """
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103 __slots__ = ['algorithm', 'algorithm_version', 'algorithm_reference','database_name',
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104 'database_letters', 'database_entries', 'parameters', 'results']
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105
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106 def __init__(self) :
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107 for name in self.__slots__ : setattr(self, name, None)
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108 self.parameters = {}
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109 self.results = []
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110
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111 def __repr__(self):
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112 return stdrepr(self)
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113
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114
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115 class Result(object) :
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116 """ The result from searching a database with a single query sequence.
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117
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118 query -- Information about the query sequence
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119 statistics -- A dictionary of search statistics
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120 hits -- A list of Hits
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121 """
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122 __slots__ = ['query', 'statistics', 'hits']
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123
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124 def __init__(self) :
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125 for name in self.__slots__ : setattr(self, name, None)
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126 self.query = Annotation()
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127 self.statistics = {}
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128 self.hits = []
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129
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130 def __repr__(self):
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131 return stdrepr(self)
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132
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133
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134 class Hit(object) :
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135 """ A search hit between a query sequence and a subject sequence.
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136 Each hit may have one or more Alignments
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137
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138 target -- Information about the target sequence.
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139 raw_score -- Typically the ignficance of the hit in bits, e.g. 92.0
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140 significance -- Typically evalue. e.g '2e-022'
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141 alignments -- A list of alignments between subject and target
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142 """
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143 __slots__ =['target', 'raw_score', 'bit_score', 'significance',
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144 'alignments']
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145 def __init__(self) :
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146 for name in self.__slots__ : setattr(self, name, None)
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147 self.target = Annotation()
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148 self.alignments = []
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149
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150 def __repr__(self):
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151 return stdrepr(self)
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152
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153 class Annotation(object) :
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154 """ Information about a subject or query sequence.
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155
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156 name -- subject sequence name, e.g. '443893|124775'
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157 description -- e.g. 'LaForas sequence'
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158 length -- subject sequence length, e.g. 331
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159 locus -- e.g. '124775'
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160 accession -- e.g. '443893'
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161 """
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162 # Fixme: change into generic sequence annotation class?
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163 __slots__ = ['name', 'description', 'length', 'locus', 'accession', ]
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164
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165 def __init__(self):
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166 for name in self.__slots__ :
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167 setattr(self, name, None)
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168
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169 def __repr__(self):
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170 return stdrepr(self)
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171
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172 class Alignment(object):
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173 """An alignment between query and subject sequences.
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174 For BLAST, these are High scoring Segment pairs (HSPs)
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175
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176 raw_score -- Typically signficance of the hit in bits, e.g. 92.0
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177 significance -- Typically evalue. e.g '2e-022'
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178
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179 similar -- number of conserved residues #FIXME eiter frac or num
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180 identical -- number of identical residues
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181 gaps -- number of gaps
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182 length -- length of the alignment
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183
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184 query_seq -- query string from alignment
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185 target_seq -- hit string from alignment
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186 mid_seq --
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187
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188 query_start --
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189 query_frame --
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190
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191 target_start --
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192 target_frame --
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193
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194 """
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195 __slots__ = ['raw_score', 'bit_score', 'significance', 'similar',
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196 'identical', 'gaps', 'length', 'query_seq', 'target_seq', 'mid_seq',
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197 'query_start', 'query_frame', 'target_start',
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198 'target_frame']
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199
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200 def __init__(self):
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201 for name in self.__slots__ :
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202 setattr(self, name, None)
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203
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204 def __repr__(self):
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205 return stdrepr(self)
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206
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207 |
