Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/coord/Match.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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202 return False |
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203 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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206 return False |