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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 import optparse
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32 import os
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33 import sys
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34 import re
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35 import datetime
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36 from commons.core.parsing.BlatParser import BlatParser
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37 from commons.core.seq.FastaUtils import FastaUtils
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38
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39 class BlatToGffForBesPaired(object):
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40
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41
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42 def __init__(self):
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43 pass
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44
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45 def setAttributesFromCmdLine(self):
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46 help = '\
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47 \nThis Script Launch BlatToGffForBesPaired.\n\n\
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48 Example 1: python BlatToGffForBesPaired.py -i blatResultsFile.tab -f besSequences.fasta -o outputFile.gff3\n\
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49 Example 2: python BlatToGffForBesPaired.py -i blatResultsFile.tab -f besSequences.fasta -o outputFile.gff3 -n muscadine:filtre1\n\n\
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50 Note 1: In blat input file, all BAC-Ends must be paired. In addition, they must be one above the other.\nFor example, if you have the BES MRRE1H032F08FM1 (forward), we must have the BES MRRE1H032F08RM1 (reverse) just after, like:\n\
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51 554\t26\t0\t0\t1\t16\t1\t17\t+\tMRRE1H032F08FM1\t606\t10\t606\tchr11\t19818926\t3725876\t3726473\t2\t553,27,\t10,579,\t3725876,3726446,\n\
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52 620\t23\t0\t0\t0\t0\t0\t0\t-\tMRRE1H032F08RM1\t643\t0\t643\tchr11\t19818926\t3794984\t3795627\t1\t643,\t0,\t3794984,\n\
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53 Note 2: the header in Blat results output file must be present (5 lines).\n\n'
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54
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55 parser = optparse.OptionParser(usage= help, version="CovertSamToFastq.py v1.0")
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56 parser.add_option( '-i', '--input', dest='inputBLAT', help='Blat Input File Name, with BES paired (1 Forward and 1 Reverse) [Format: tabular]', default= None )
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57 parser.add_option( '-f', '--fasta', dest='inputFASTA', help='Fasta Input File Name, with all sequences of BES [Format: fasta]', default= None )
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58 parser.add_option( '-o', '--output', dest='output', help='Output File Name [Format: GFF3]', default= None )
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59 parser.add_option( '-n', '--methodname', dest='methodName', help='Method name in col. 3 [Default: None]', default= None )
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60 ( options, args ) = parser.parse_args()
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61 self._options = options
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62
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63 def checkOptions(self):
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64 if self._options.inputBLAT == '':
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65 raise Exception("ERROR: No Blat file specified for -i !")
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66 elif not os.path.exists(self._options.inputBLAT):
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67 raise Exception("ERROR: Blat Input File doesn't exist !")
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68 else:
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69 self._inputFileBlat = self._options.inputBLAT
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70
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71 if self._options.inputFASTA == '':
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72 raise Exception("ERROR: No Fasta file specified for -f !")
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73 elif not os.path.exists(self._options.inputFASTA):
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74 raise Exception("ERROR: Fasta Input File doesn't exist !")
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75 else:
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76 self._inputFileFasta = self._options.inputFASTA
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77
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78 if self._options.output == '':
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79 raise Exception("ERROR: No Output file specified for -o !")
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80 else:
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81 self._outputFileGFF = self._options.output
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82
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83 self._methodName = self._options.methodName
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84
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85 def run(self):
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86 self.checkOptions()
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87 self._createGFFOutputFile()
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88 BLATFile = open(self._inputFileBlat, 'r')
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89
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90 headerBlatLine = BLATFile.readline()
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91 headerBlatLine = BLATFile.readline()
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92 headerBlatLine = BLATFile.readline()
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93 headerBlatLine = BLATFile.readline()
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94 headerBlatLine = BLATFile.readline()
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95 blatLine = BLATFile.readline()
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96 numberLine = 6
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97 while blatLine != '':
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98 lGffLines = []
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99
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100 gffLineBes1, besName1, seqBes1, typeBes1 = self.convertBlatObjectToGffLine(blatLine, numberLine)
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101 lGffLines.append(gffLineBes1)
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102
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103 blatLine = BLATFile.readline()
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104 numberLine = numberLine + 1
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105
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106 gffLineBes2, besName2, seqBes2, typeBes2 = self.convertBlatObjectToGffLine(blatLine, numberLine)
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107 lGffLines.append(gffLineBes2)
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108
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109 gffLineBac = self.createGffLineForBac(gffLineBes1, besName1, seqBes1, typeBes1, gffLineBes2, besName2, seqBes2, typeBes2, numberLine)
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110 lGffLines.append(gffLineBac)
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111
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112 if gffLineBac != None:
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113 self._printGFFLinesToOutputFile(lGffLines)
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114
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115 blatLine = BLATFile.readline()
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116 numberLine = numberLine + 1
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117
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118 def convertBlatObjectToGffLine(self, blatLine, numberLine):
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119 iBlatHit = BlatParser()
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120 iBlatHit.setAttributesFromString(blatLine, numberLine)
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121 besName = iBlatHit.getQName()
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122 seqBes = self.extractBesSequenceFromFastaFile(besName, numberLine)
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123
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124 typeBes = ''
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125 if re.match('^.+FM[0-9]$', besName):
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126 typeBes = 'FM'
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127 elif re.match('^.+RM[0-9]$', besName):
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128 typeBes = 'RM'
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129
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130 col1 = iBlatHit.getTName()
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131 col2 = 'BlatToGffForBesPaired'
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132 if self._methodName == '' or self._methodName == None:
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133 col3 = 'BES'
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134 else:
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135 col3 = '%s:BES' % self._methodName
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136 col4 = iBlatHit.getTStart()
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137 col5 = iBlatHit.getTEnd()
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138 col6 = '.'
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139 col7 = '+'
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140 col8 = '.'
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141 col9 = 'ID=%s;Name=%s;bes_start=%s;bes_end=%s;bes_size=%s;muscadine_seq=%s' % (besName, besName, iBlatHit.getTStart(), iBlatHit.getTEnd(), iBlatHit.getTSize(), seqBes)
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142
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143 gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9)
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144 return gffLine, iBlatHit.getQName(),seqBes, typeBes
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145
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146 def createGffLineForBac(self, gffLineBes1, besName1, seqBes1, typeBes1, gffLineBes2, besName2, seqBes2, typeBes2, numberLine):
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147 lGffLineBes1 = gffLineBes1.split('\t')
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148 lGffLineBes2 = gffLineBes2.split('\t')
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149 besName1 = self.getBesName(lGffLineBes1[8])
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150 besName2 = self.getBesName(lGffLineBes2[8])
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151
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152 tBes1 = (lGffLineBes1[0], int(lGffLineBes1[3]), int(lGffLineBes1[4]))
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153 tBes2 = (lGffLineBes2[0], int(lGffLineBes2[3]), int(lGffLineBes2[4]))
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154
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155 if self.checkBesNames(besName1, besName2, numberLine) == True and self.checkBesPositions(tBes1, tBes2) == True:
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156 startBacPos, endBacPos = self.getBacPositions(tBes1, tBes2)
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157 sizeBacPos = endBacPos - startBacPos + 1
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158 bacName = self.getBacName(besName1)
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159 nameBesFM, seqBesFM, nameBesRM, seqBesRM = self.getBesFmAndRmNamesAndSequences(besName1, seqBes1, typeBes1, besName2, seqBes2, typeBes2)
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160
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161 col1 = lGffLineBes1[0]
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162 col2 = 'BlatToGffForBesPaired'
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163 if self._methodName == '' or self._methodName == None:
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164 col3 = 'BAC'
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165 else:
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166 col3 = '%s:BAC' % self._methodName
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167 col4 = startBacPos
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168 col5 = endBacPos
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169 col6 = '.'
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170 col7 = '.'
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171 col8 = '.'
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172 col9 = 'ID=%s;Name=%s;bac_start=%s;bac_end=%s;bac_size=%s;besFM_name=%s;muscadine_besFM_seq=%s;besRM_name=%s;muscadine_besRM_seq=%s' % (bacName, bacName, startBacPos, endBacPos, sizeBacPos, nameBesFM, seqBesFM, nameBesRM, seqBesRM)
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173 gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9)
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174 return gffLine
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175 return None
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176
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177 def getBesFmAndRmNamesAndSequences(self, besName1, seqBes1, typeBes1, besName2, seqBes2, typeBes2):
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178 if typeBes1 == 'FM' and typeBes2 == 'RM':
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179 return besName1, seqBes1, besName2, seqBes2
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180 elif typeBes1== 'RM' and typeBes2 == 'FM':
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181 return besName2, seqBes2, besName1, seqBes1
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182
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183 def getBesName(self, col9):
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184 lCol9 = col9.split(';')
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185 ID = lCol9[0]
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186 besName = ID[3:]
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187 return besName
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188
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189 def getBacName(self, besName):
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190 bacName = besName[:-3]
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191 return bacName
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192
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193 def checkBesNames(self, besName1, besName2, line):
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194 bacName1 = besName1[:-3]
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195 bacName2 = besName2[:-3]
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196 if bacName1 == bacName2:
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197 return True
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198 else:
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199 sys.stderr.write("WARNING: Lines %s and %s the two Bes (%s AND %s) do not belong to the same BAC !!!\n -> you have to filter this Blat file...\n" % (int(line)-1, line, besName1, besName2))
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200 return False
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201
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202 def checkBesPositions(self, tBes1, tBes2):
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203 if tBes1[0] == tBes2[0]:
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204 minBes1 = min(tBes1[1], tBes1[2])
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205 maxBes1 = max(tBes1[1], tBes1[2])
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206 minBes2 = min(tBes2[1], tBes2[2])
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207 maxBes2 = max(tBes2[1], tBes2[2])
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208 if (minBes1 < minBes2 and maxBes1 < minBes2) or (minBes2 < minBes1 and maxBes2 < minBes1):
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209 return True
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210 return False
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211
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212 def getBacPositions(self, tBes1, tBes2):
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213 startBacPos = 0
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214 endBacPos = 0
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215 minBes1 = min(tBes1[1], tBes1[2])
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216 maxBes1 = max(tBes1[1], tBes1[2])
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217 minBes2 = min(tBes2[1], tBes2[2])
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218 maxBes2 = max(tBes2[1], tBes2[2])
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219 if minBes1 < minBes2:
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220 startBacPos = minBes1
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221 endBacPos = maxBes2
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222 else:
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223 startBacPos = minBes2
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224 endBacPos = maxBes1
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225 return startBacPos, endBacPos
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226
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227 def extractBesSequenceFromFastaFile(self, besName, numberLine):
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228 seq = ''
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229 date = datetime.datetime.now()
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230 date = date.strftime("%d%m%Y_%H%M%S")
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231 tmpFileName = 'tmp_BlatToGffForBesPaired_%s.fasta' % date
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232 iFastaUtils = FastaUtils()
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233 iFastaUtils.dbExtractByPattern(besName, self._inputFileFasta, tmpFileName)
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234
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235 if os.path.exists(tmpFileName):
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236 newFastaFile = open(tmpFileName, 'r')
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237 line = newFastaFile.readline()
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238 if line != '':
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239 while line != '':
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240 if line[0] != '>':
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241 line = line.replace('\n', '')
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242 seq += line
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243 line = newFastaFile.readline()
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244 newFastaFile.close()
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245 os.remove(tmpFileName)
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246 return seq
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247 os.remove(tmpFileName)
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248
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249 sys.stderr.write("WARNING: At line %s, the BAC-Ends (%s) hasn't got sequence in fasta file (%s) !!\n" % (numberLine, besName, os.path.basename(self._inputFileFasta)))
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250 return 'NA'
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251
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252 def _createGFFOutputFile(self):
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253 GFFfile = open(self._outputFileGFF, 'w')
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254 GFFfile.write("##gff-version 3\n")
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255 GFFfile.close()
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256
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257 def _printGFFLinesToOutputFile(self, lLines):
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258 GFFfile = open(self._outputFileGFF, 'a')
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259 for line in lLines:
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260 GFFfile.write(line)
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261 GFFfile.close()
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262
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263 if __name__ == '__main__':
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264 iBlatToGffForBesPaired = BlatToGffForBesPaired()
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265 iBlatToGffForBesPaired.setAttributesFromCmdLine()
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266 iBlatToGffForBesPaired.run() |
