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18
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1 #!/usr/bin/env python
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2
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3 import sys
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4 import os
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5 import getopt
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6
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7 from commons.core.sql.DbMySql import DbMySql
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8 from commons.core.seq.FastaUtils import FastaUtils
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9 from commons.core.coord.MapUtils import MapUtils
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10 from commons.core.coord.AlignUtils import AlignUtils
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11 from commons.core.coord.PathUtils import PathUtils
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12
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13
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14 class SpliceTEsFromGenome( object ):
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15
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16 def __init__( self ):
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17 self._inputData = ""
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18 self._formatData = ""
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19 self._genomeFile = ""
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20 self._configFile = ""
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21 self._outFile = ""
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22 self._verbose = 0
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23 self._db = None
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24
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25
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26 def help( self ):
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27 print
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28 print "usage: SpliceTEsFromGenome.py [ options ]"
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29 print "options:"
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30 print " -h: this help"
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31 print " -i: input TE coordinates (can be file or table)"
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32 print " TEs as subjects if align or path format"
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33 print " -f: format of the data (map/align/path)"
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34 print " -g: genome file (format=fasta)"
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35 print " -C: configuration file (if table as input)"
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36 print " -o: output fasta file (default=genomeFile+'.splice')"
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37 print " -v: verbosity level (default=0/1)"
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38 print
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39
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40
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41 def setAttributesFromCmdLine( self ):
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42 try:
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43 opts, args = getopt.getopt(sys.argv[1:],"hi:f:g:C:o:v:")
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44 except getopt.GetoptError, err:
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45 msg = "%s" % str(err)
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46 sys.stderr.write( "%s\n" % msg )
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47 self.help(); sys.exit(1)
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48 for o,a in opts:
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49 if o == "-h":
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50 self.help(); sys.exit(0)
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51 elif o == "-i":
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52 self._inputData = a
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53 elif o == "-f":
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54 self._formatData = a
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55 elif o == "-g":
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56 self._genomeFile = a
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57 elif o == "-C":
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58 self._configFile = a
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59 elif o =="-o":
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60 self._outFile = a
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61 elif o == "-v":
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62 self._verbose = int(a)
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63
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64
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65 def checkAttributes( self ):
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66 if self._inputData == "":
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67 msg = "ERROR: missing input data (-i)"
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68 sys.stderr.write( "%s\n" % msg )
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69 self.help()
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70 sys.exit(1)
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71 if not os.path.exists( self._inputData ):
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72 if not os.path.exists( self._configFile ):
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73 msg = "ERROR: neither input file '%s' nor configuration file '%s'" % ( self._inputData, self._configFile )
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74 sys.stderr.write( "%s\n" % msg )
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75 self.help()
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76 sys.exit(1)
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77 if not os.path.exists( self._configFile ):
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78 msg = "ERROR: can't find config file '%s'" % ( self._configFile )
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79 sys.stderr.write( "%s\n" % msg )
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80 sys.exit(1)
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81 self._db = DbMySql( cfgFileName=self._configFile )
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82 if not self._db.doesTableExist( self._inputData ):
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83 msg = "ERROR: can't find table '%s'" % ( self._inputData )
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84 sys.stderr.write( "%s\n" % msg )
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85 self.help()
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86 sys.exit(1)
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87 if self._formatData == "":
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88 msg = "ERROR: need to precise format (-f)"
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89 sys.stderr.write( "%s\n" % msg )
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90 self.help()
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91 sys.exit(1)
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92 if self._formatData not in [ "map", "align", "path" ]:
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93 msg = "ERROR: format '%s' not yet supported" % ( self._formatData )
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94 sys.stderr.write( "%s\n" % msg )
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95 self.help()
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96 sys.exit(1)
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97 if self._genomeFile == "":
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98 msg = "ERROR: missing genome file (-g)"
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99 sys.stderr.write( "%s\n" % msg )
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100 self.help()
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101 sys.exit(1)
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102 if not os.path.exists( self._genomeFile ):
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103 msg = "ERROR: can't find genome file '%s'" % ( self._genomeFile )
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104 sys.stderr.write( "%s\n" % msg )
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105 self.help()
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106 sys.exit(1)
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107 if self._outFile == "":
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108 self._outFile = "%s.splice" % ( self._genomeFile )
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109 if self._verbose > 0:
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110 print "output fasta file: %s" % self._outFile
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111
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112
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113 def getCoordsAsMapFile( self ):
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114 if self._verbose > 0:
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115 print "get TE coordinates as 'Map' file"
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116 sys.stdout.flush()
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117 if self._db != None:
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118 cmd = "srptExportTable.py"
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119 cmd += " -i %s" % ( self._inputData )
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120 cmd += " -C %s" % ( self._configFile )
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121 cmd += " -o %s.%s" % ( self._inputData, self._formatData )
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122 returnStatus = os.system( cmd )
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123 if returnStatus != 0:
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124 msg = "ERROR while exporting data from table"
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125 sys.stderr.write( "%s\n" % msg )
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126 sys.exit(1)
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127 self._inputData += ".%s" % ( self._formatData )
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128
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129 if self._formatData == "map":
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130 return self._inputData
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131 elif self._formatData == "align":
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132 mapFile = "%s.map" % ( self._inputData )
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133 AlignUtils.convertAlignFileIntoMapFileWithSubjectsOnQueries( self._inputData, mapFile )
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134 return mapFile
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135 elif self._formatData == "path":
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136 mapFile = "%s.map" % ( self._inputData )
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137 PathUtils.convertPathFileIntoMapFileWithSubjectsOnQueries( self._inputData, mapFile )
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138 return mapFile
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139
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140
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141 def mergeCoordsInMapFile( self, mapFile ):
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142 if self._verbose > 0:
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143 print "merge TE coordinates"
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144 sys.stdout.flush()
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145 mergeFile = "%s.merge" % ( mapFile )
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146 MapUtils.mergeCoordsInFile( mapFile, mergeFile )
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147 if self._formatData != "map" or self._db != None:
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148 os.remove( mapFile )
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149 return mergeFile
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150
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151
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152 def spliceFastaFromCoords( self, mergeFile ):
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153 if self._verbose > 0:
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154 print "splice TE copies from the genome"
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155 sys.stdout.flush()
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156 FastaUtils.spliceFromCoords( self._genomeFile,
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157 mergeFile,
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158 self._outFile )
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159
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160 os.remove( mergeFile )
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161
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162
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163 def start( self ):
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164 self.checkAttributes()
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165 if self._verbose > 0:
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166 print "START SpliceTEsFromGenome.py"
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167 sys.stdout.flush()
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168
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169
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170 def end( self ):
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171 if self._db != None:
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172 self._db.close()
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173 if self._verbose > 0:
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174 print "END SpliceTEsFromGenome.py"
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175 sys.stdout.flush()
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176
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177
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178 def run( self ):
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179 self.start()
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180
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181 mapFile = self.getCoordsAsMapFile()
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182
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183 mergeFile = self.mergeCoordsInMapFile( mapFile )
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184
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185 self.spliceFastaFromCoords( mergeFile )
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186
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187 self.end()
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188
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189
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190 if __name__ == "__main__":
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191 i = SpliceTEsFromGenome()
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192 i.setAttributesFromCmdLine()
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193 i.run()
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