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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 import sys
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33 from commons.core.coord.Range import Range
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34 from commons.core.coord.Path import Path
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35
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36
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37 ## Handle a chain of match(es) between two sequences, query and subject, with an identifier and the length of the input sequences
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38 #
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39 class Match( Path ):
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40
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41 ## Constructor
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42 #
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43 def __init__(self):
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44 Path.__init__(self)
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45 self.query_length = -1
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46 self.query_length_perc = -1 # length of the match on the query / length of the query
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47 self.query_seqlength = -1
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48 self.match_length_perc = -1 # length of the match on the query / total length of the subject
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49 self.subject_length = -1
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50 self.subject_length_perc = -1 # length of the match on the subject / length of the subject
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51 self.subject_seqlength = -1
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52
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53 ## Equal operator
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54 #
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55 def __eq__(self, o):
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56 if o == None \
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57 or self.query_length != o.query_length or self.query_length_perc != o.query_length_perc\
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58 or self.query_seqlength != o.query_seqlength or self.subject_length != o.subject_length\
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59 or self.subject_length_perc != o.subject_length_perc or self.subject_seqlength != o.subject_seqlength\
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60 or self.match_length_perc != o.match_length_perc:
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61 return False
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62 return Path.__eq__(self, o)
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63
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64 ## Return the length of the match on the query divided by the total length of the query
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65 #
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66 def getLengthPercOnQuery(self):
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67 return self.query_length_perc
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68
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69 ## Return the length of the match on the subject divided by the total length of the subject
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70 #
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71 def getLengthPercOnSubject(self):
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72 return self.subject_length_perc
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73
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74 ## Return the length of the match on the subject
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75 #
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76 def getLengthMatchOnSubject(self):
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77 return self.subject_length
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78
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79 ## Set attributes from a tuple
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80 #
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81 # @param tuple: a tuple with (query name,query start,query end,
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82 # query length, query length perc (between 0-1), match length perc (between 0-1), subject name,
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83 # subject start,subject end,subject length, subject length percentage (between 0-1), e_value,score,identity,id)
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84 #
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85 def setFromTuple( self, tuple ):
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86 queryStart = int(tuple[1])
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87 queryEnd = int(tuple[2])
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88 subjectStart = int(tuple[7])
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89 subjectEnd = int(tuple[8])
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90 if queryStart < queryEnd:
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91 self.range_query = Range(tuple[0],queryStart,queryEnd)
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92 self.range_subject = Range(tuple[6],subjectStart,subjectEnd)
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93 else:
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94 self.range_query = Range(tuple[0],queryEnd,queryStart)
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95 self.range_subject = Range(tuple[6],subjectEnd,subjectStart)
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96 self.query_length = int(tuple[3])
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97 self.query_length_perc = float(tuple[4])
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98 self.query_seqlength = int( self.query_length / self.query_length_perc )
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99 self.match_length_perc = float(tuple[5])
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100 self.subject_length = int(tuple[9])
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101 self.subject_length_perc = float(tuple[10])
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102 self.subject_seqlength = int( self.subject_length / self.subject_length_perc )
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103 self.e_value = float(tuple[11])
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104 self.score = float(tuple[12])
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105 self.identity = float(tuple[13])
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106 self.id = int(tuple[14])
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107
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108 ## Reset
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109 #
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110 def reset( self ):
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111 Path.reset( self )
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112 self.query_length = -1
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113 self.query_length_perc = -1
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114 self.query_seqlength = -1
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115 self.match_length_perc = -1
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116 self.subject_length = -1
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117 self.subject_length_perc = -1
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118 self.subject_seqlength = -1
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119
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120 ## Return a formated string of the attribute data
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121 #
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122 def toString( self ):
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123 string = "%s" % ( self.range_query.toString() )
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124 string += "\t%i\t%f" % ( self.query_length,
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125 self.query_length_perc )
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126 string += "\t%f" % ( self.match_length_perc )
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127 string += "\t%s" % ( self.range_subject.toString() )
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128 string += "\t%i\t%f" % ( self.subject_length,
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129 self.subject_length_perc )
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130 string += "\t%g\t%i\t%f" % ( self.e_value,
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131 self.score,
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132 self.identity )
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133 string += "\t%i" % ( self.id )
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134 return string
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135
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136 ## Return a Path instance
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137 #
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138 def getPathInstance( self ):
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139 p = Path()
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140 tuple = ( self.id,
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141 self.range_query.seqname,
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142 self.range_query.start,
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143 self.range_query.end,
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144 self.range_subject.seqname,
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145 self.range_subject.start,
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146 self.range_subject.end,
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147 self.e_value,
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148 self.score,
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149 self.identity )
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150 p.setFromTuple( tuple )
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151 return p
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152
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153 ## Give information about a match whose query is included in the subject
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154 #
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155 # @return string
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156 #
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157 def getQryIsIncluded( self ):
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158 string = "query %s (%d bp: %d-%d) is contained in subject %s (%d bp: %d-%d): id=%.2f - %.3f - %.3f - %.3f" %\
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159 ( self.range_query.seqname, self.query_seqlength, self.range_query.start, self.range_query.end,
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160 self.range_subject.seqname, self.subject_seqlength, self.range_subject.start, self.range_subject.end,
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161 self.identity, self.query_length_perc, self.match_length_perc, self.subject_length_perc )
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162 return string
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163
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164 def increaseLengthPercOnQuery(self, coverage):
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165 self.query_length_perc += coverage
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166
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167 ## Compare the object with another match and see if they are equal
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168 # (same identity, E-value and score + same subsequences whether in query or subject)
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169 #
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170 # @return True if objects are equals False otherwise
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171 #
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172 def isDoublonWith( self, match, verbose=0 ):
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173
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174 # if both matches have same identity, score and E-value
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175 if self.identity == match.identity and self.score == match.score and self.e_value == match.e_value:
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176
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177 # if query and subject are identical
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178 if ( self.range_query.seqname == match.range_query.seqname \
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179 and self.range_subject.seqname == match.range_subject.seqname ):
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180
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181 # if the coordinates are equal
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182 if self.range_query.__eq__( match.range_query ) and self.range_subject.__eq__( match.range_subject ):
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183 return True
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184
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185 else:
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186 if verbose > 0: print "different coordinates"; sys.stdout.flush()
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187 return False
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188
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189 # if query and subject are reversed but identical
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190 elif self.range_query.seqname == match.range_subject.seqname and self.range_subject.seqname == match.range_query.seqname:
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191
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192 # if the coordinates are equal
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193 if self.range_query.__eq__( match.range_subject ) and self.range_subject.__eq__( match.range_query ):
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194 return True
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195
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196 else:
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197 if verbose > 0: print "different coordinates"; sys.stdout.flush()
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198 return False
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199
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200 else:
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201 if verbose > 0: print "different sequence names"; sys.stdout.flush()
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202 return False
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203
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204 else:
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205 if verbose > 0: print "different match numbers"; sys.stdout.flush()
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206 return False
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