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1 #!/usr/bin/env python
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2
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3 # Copyright INRA (Institut National de la Recherche Agronomique)
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4 # http://www.inra.fr
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5 # http://urgi.versailles.inra.fr
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6 #
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7 # This software is governed by the CeCILL license under French law and
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8 # abiding by the rules of distribution of free software. You can use,
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9 # modify and/ or redistribute the software under the terms of the CeCILL
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10 # license as circulated by CEA, CNRS and INRIA at the following URL
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11 # "http://www.cecill.info".
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12 #
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13 # As a counterpart to the access to the source code and rights to copy,
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14 # modify and redistribute granted by the license, users are provided only
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15 # with a limited warranty and the software's author, the holder of the
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16 # economic rights, and the successive licensors have only limited
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17 # liability.
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18 #
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19 # In this respect, the user's attention is drawn to the risks associated
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20 # with loading, using, modifying and/or developing or reproducing the
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21 # software by the user in light of its specific status of free software,
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22 # that may mean that it is complicated to manipulate, and that also
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23 # therefore means that it is reserved for developers and experienced
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24 # professionals having in-depth computer knowledge. Users are therefore
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25 # encouraged to load and test the software's suitability as regards their
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26 # requirements in conditions enabling the security of their systems and/or
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27 # data to be ensured and, more generally, to use and operate it in the
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28 # same conditions as regards security.
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29 #
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30 # The fact that you are presently reading this means that you have had
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31 # knowledge of the CeCILL license and that you accept its terms.
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32
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33 from commons.core.LoggerFactory import LoggerFactory
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34 from commons.core.utils.RepetOptionParser import RepetOptionParser
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35 from commons.core.checker.ConfigChecker import ConfigRules
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36 from commons.core.checker.ConfigChecker import ConfigChecker
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37 import subprocess
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38 import os
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39 from commons.core.seq.Bioseq import Bioseq
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40
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41 LOG_DEPTH = "repet.core.launchers"
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42
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43 from commons.core.seq.BioseqDB import BioseqDB
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44 from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
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45
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46
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47 class LaunchRefAlign(object):
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48 """
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49 Launch 'refalign' to build a master-slave multiple sequence alignment.
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50 """
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51 def __init__(self, inputFileName="", outFileName="", gapSize=10, match=10, mismatch=8, gapOpen=16, gapExtend=4, refseqName="", keepRefseq =False, verbosity=3 ):
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52 self.inputFileName = inputFileName
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53 self.outFileName=outFileName
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54 self.gapSize = gapSize
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55 self.match = match
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56 self.mismatch = mismatch
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57 self.gapOpen = gapOpen
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58 self.gapExtend = gapExtend
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59 self.gapExtend = gapExtend
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60 self.refseqName = refseqName
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61 self.keepRefseq = keepRefseq
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62 self._verbosity = verbosity
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63 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
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64
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65 def setAttributesFromCmdLine(self):
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66 description = "usage: LaunchRefalign.py [ options ]"
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67 epilog = "\n -h: this help\n"
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68 epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
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69 epilog += "\t -r: keep the reference sequence"
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70 epilog += "\t -o: name of the output file (default=inFileName+'.fa_aln')"
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71 epilog += "\t -v: verbosity (default=0)"
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72 epilog += "\n\t"
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73 parser = RepetOptionParser(description = description, epilog = epilog)
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74 parser.add_option("-i", "--fasta", dest = "inputFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
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75 parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output file name [default: <input>.out]", default = "")
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76 parser.add_option("-r", "--keepRefseq", dest = "keepRefseq", action = "store_true", help = "keep reference sequence [optional] [default: False]", default = False)
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77 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1)
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78 options = parser.parse_args()[0]
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79 self._setAttributesFromOptions(options)
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80
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81 def _setAttributesFromOptions(self, options):
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82 self.inputFileName = options.inputFileName
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83 self.setOutFileName = options.outFileName
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84 self.keepRefseq = options.keepRefseq
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85 self._verbosity = options.verbosity
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86
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87 def _checkOptions(self):
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88 if self.inputFileName == "":
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89 self._logAndRaise("ERROR: Missing input file name")
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90
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91 if self.outFileName == "":
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92 self.outFileName = "%s.fa_aln" % (self.inputFileName)
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93
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94 def _logAndRaise(self, errorMsg):
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95 self._log.error(errorMsg)
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96 raise Exception(errorMsg)
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97
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98 def _prepareRefAlign(self):
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99 self.shortInputFileName = self.inputFileName+".shortH"
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100 self.refFileName= self.shortInputFileName + ".ref"
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101 self.cpyFileName=self.shortInputFileName + ".cpy"
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102
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103 file_db = open(self.shortInputFileName)
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104 file_ref = open(self.refFileName,"w")
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105 file_cpy = open(self.cpyFileName,"w")
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106
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107 self._numseq=0
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108 while 1:
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109 seq=Bioseq()
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110 seq.read(file_db)
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111 if seq.sequence==None:
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112 break
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113 self._numseq+=1
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114 if self._numseq==1:
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115 seq.write(file_ref)
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116 else:
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117 seq.write(file_cpy)
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118 file_db.close()
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119 file_ref.close()
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120 file_cpy.close()
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121
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122 def _shortenHeaders(self):
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123 self.csh = ChangeSequenceHeaders()
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124 self.csh.setInputFile(self.inputFileName)
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125 self.csh.setFormat("fasta")
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126 self.csh.setStep(1)
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127 self.csh.setPrefix("seq")
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128 self.csh.setLinkFile(self.inputFileName+".shortHlink")
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129 self.csh.setOutputFile(self.inputFileName+".shortH")
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130 self.csh.setVerbosityLevel(self._verbosity-1)
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131 self.csh.run()
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132
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133 bsDB = BioseqDB(self.inputFileName+".shortH")
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134 bsDB.upCase()
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135 bsDB.save(self.inputFileName+".shortHtmp")
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136 del bsDB
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137 os.rename(self.inputFileName+".shortHtmp", self.inputFileName+".shortH")
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138
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139 def _renameHeaders(self):
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140 self.csh.setInputFile(self.inputFileName+".shortH.fa_aln")
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141 self.csh.setFormat("fasta")
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142 self.csh.setStep(2)
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143 self.csh.setLinkFile(self.inputFileName+".shortHlink" )
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144 self.csh.setOutputFile(self.outFileName)
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145 self.csh.setVerbosityLevel(self._verbosity-1)
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146 self.csh.run()
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147
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148 def run(self):
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149 LoggerFactory.setLevel(self._log, self._verbosity)
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150 self._checkOptions()
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151 self._log.info("START LaunchRefAlign")
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152 self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName))
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153
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154 inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName))
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155 if not os.path.exists(inputFileName):
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156 os.symlink(self.inputFileName, inputFileName)
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157 self.inputFileName = inputFileName
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158
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159 self._shortenHeaders()
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160 if self.keepRefseq:
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161 self.refseqName="seq1"
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162 self._prepareRefAlign()
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163
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164 if self._numseq > 1:
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165 cmd = "refalign %s %s -m %d -l %d -d %d -g %d -e %d" % (self.refFileName, self.cpyFileName, self.match, self.gapSize, self.mismatch, self.gapOpen, self.gapExtend)
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166
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167 process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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168 self._log.debug("Running : %s" % cmd)
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169 output = process.communicate()
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170 self._log.debug("Output:\n%s" % output[0])
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171 if process.returncode != 0:
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172 self._logAndRaise("ERROR when launching '%s'" % cmd)
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173 refseqNameParam = ""
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174 if self.refseqName != "":
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175 refseqNameParam = "-r %s " % (self.refseqName)
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176 outFileName = self.inputFileName+".shortH.fa_aln"
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177 #self.cpyFileName = os.path.join(os.getcwd(),os.path.basename(self.cpyFileName))
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178
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179 self._log.info("Copy file path %s " % self.cpyFileName)
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180 print("Copy file path %s " % self.cpyFileName)
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181 cmd = "refalign2fasta.py -i %s.aligner %s-g d -o %s -v 1" % (self.cpyFileName, refseqNameParam, outFileName)
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182 self._log.debug("Running : %s" % cmd)
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183 process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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184 output = process.communicate()
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185 self._log.debug("Output:\n%s" % output[0])
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186
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187 if process.returncode != 0:
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188 self._logAndRaise("ERROR when launching '%s'" % cmd)
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189
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190 cmd = "rm -f "+ self.refFileName + " " + self.cpyFileName + " " + self.cpyFileName + ".aligner " + self.cpyFileName + ".oriented " + self.cpyFileName + ".refalign.stat"
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191 os.system(cmd)
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192
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193 else:
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194 self._logAndRaise("Only one sequence available")
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195 cmd = "echo empty"
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196
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197 self._renameHeaders()
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198
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199 for fileName in [self.inputFileName + ".shortH", self.inputFileName + ".shortHlink", self.inputFileName + ".shortH.fa_aln"]:
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200 os.remove(fileName)
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201 self._log.info("END LaunchRefAlign")
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202 return 0
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203
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204
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205 if __name__ == "__main__":
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206 iLaunchRefAlign = LaunchRefAlign()
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207 iLaunchRefAlign.setAttributesFromCmdLine()
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208 iLaunchRefAlign.run()
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