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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 import os
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34 import sys
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35 from ConfigParser import NoSectionError, NoOptionError
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36 from commons.core.checker.CheckerUtils import CheckerUtils
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37 from commons.core.checker.CheckerException import CheckerException
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38 from commons.core.utils.FileUtils import FileUtils
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39 from commons.core.seq.FastaUtils import FastaUtils
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40
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41 class PrepareBatches(object):
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42
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43 def __init__(self, pipelineName, projectDir, projectName, iConfig, verbose):
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44 self._pipelineName = pipelineName
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45 self._projectDir = projectDir
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46 self._projectName = projectName
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47 self._iConfig = iConfig
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48 self._verbose = verbose
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49
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50 def run(self):
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51 if self._verbose > 0:
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52 print "beginning of step 1"
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53 sys.stdout.flush()
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54 if FileUtils.isRessourceExists("%s_db" % self._projectName):
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55 print "ERROR: directory '%s_db' already exists" % self._projectName
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56 sys.exit(1)
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57
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58 os.mkdir("%s_db" % self._projectName)
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59 os.chdir("%s_db" % self._projectName)
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60 genomeFastaFileName = "%s.fa" % self._projectName
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61 os.symlink("../%s" % genomeFastaFileName, genomeFastaFileName)
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62 sectionName = "prepare_batches"
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63 self._checkConfig(sectionName)
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64
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65 separator = "\n"
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66 inGenomeFileHandler = open(genomeFastaFileName, "r")
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67 try:
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68 CheckerUtils.checkHeaders(inGenomeFileHandler)
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69 except CheckerException, e:
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70 print "Error in file %s. Wrong headers are :" % genomeFastaFileName
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71 print separator.join(e.messages)
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72 print "Authorized characters are : a-z A-Z 0-9 - . : _\n"
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73 inGenomeFileHandler.close()
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74 sys.exit(1)
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75 inGenomeFileHandler.close()
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76
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77 doClean = False
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78 if self._iConfig.get(sectionName, "clean") == "yes":
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79 doClean = True
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80 chunkFilePrefix = "%s_chunks" % self._projectName
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81 chunkLength = int(self._iConfig.get(sectionName, "chunk_length"))
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82 chunkOverlap = int(self._iConfig.get(sectionName, "chunk_overlap"))
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83 FastaUtils.dbChunks(genomeFastaFileName, chunkLength, chunkOverlap, 0, chunkFilePrefix, doClean, self._verbose)
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84
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85 nbSeq = int(self._iConfig.get(sectionName, "nb_seq_per_batch"))
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86 FastaUtils.splitFastaFileInBatches("%s.fa" % chunkFilePrefix, nbSeq * chunkLength)
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87
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88 if self._iConfig.get(sectionName, "clean") == "yes":
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89 FileUtils.removeFilesByPattern("%s.fa*" % self._projectName)
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90
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91 os.chdir( ".." )
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92 if self._verbose > 0:
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93 print "step 1 finished successfully"
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94 sys.stdout.flush()
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95
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96 def _checkConfig(self, sectionName):
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97 try:
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98 CheckerUtils.checkSectionInConfigFile(self._iConfig, sectionName)
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99 except NoSectionError:
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100 print "ERROR: the section %s must be in your configuration file" % sectionName
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101 sys.exit(1)
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102 try:
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103 CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_length")
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104 except NoOptionError:
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105 print "ERROR: the option 'chunk_length' must be defined in %s in your configuration file" % sectionName
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106 sys.exit(1)
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107 try:
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108 CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "chunk_overlap")
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109 except NoOptionError:
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110 print "ERROR: the option 'chunk_overlap' must be defined in %s in your configuration file" % sectionName
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111 sys.exit(1)
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112 try:
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113 CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "nb_seq_per_batch")
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114 except NoOptionError:
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115 print "ERROR: the option 'nb_seq_per_batch' must be defined in %s in your configuration file" % sectionName
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116 sys.exit(1)
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117 try:
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118 CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "resources")
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119 except NoOptionError:
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120 print "ERROR: the option 'resources' must be defined in %s in your configuration file" % sectionName
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121 sys.exit(1)
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122 try:
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123 CheckerUtils.checkOptionInSectionInConfigFile(self._iConfig, sectionName, "tmpDir")
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124 except NoOptionError:
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125 print "ERROR: the option 'tmpDir' must be defined in %s in your configuration file" % sectionName
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126 sys.exit(1)
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