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1 #!/usr/bin/env python
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2
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3 import sys, os, optparse, shutil, glob
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4
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5 __version__ = "1.0.0"
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6 # in the case of collections, exitcodes equal to 0 and 1 are not considered errors
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7 ERR_EXIT_CODE = 2
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8 OK_EXIT_CODE = 0
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9 VALID_CHARS = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
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10
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11 def printLog( logfilepath, message, exitcode=OK_EXIT_CODE, exit=False ):
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12 print message
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13 with open( logfilepath, 'a+' ) as out:
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14 out.write( message + '\n' )
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15 if exit:
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16 sys.exit( exitcode )
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17
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18 def downloadAccessions(formats, filepaths, outlogfile, outdirpath):
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19 downloaded_files = { }
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20 for dataset_idx in range(0, len(formats)):
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21 if formats[ dataset_idx ] == 'accessions':
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22 print filepaths[ dataset_idx ]
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23 with open( filepaths[ dataset_idx ] ) as accessions:
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24 for line in accessions:
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25 print line
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26 accession = line.split( '\t' )[0].strip()
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27 if accession:
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28 printLog( outlogfile, 'Downloading \"' + accession.upper() + '\" with the fastq-dump tool (part of the sra-tools utility)' )
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29 fastq_dump_exitcode = os.system( 'fastq-dump --outdir ' + outdirpath + ' --fasta ' + accession.upper() )
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30 if fastq_dump_exitcode > 0:
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31 printLog( outlogfile, '> FASTA file: FAILED ( \"' + accession.upper() + '\" will be excluded )' )
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32 else:
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33 #os.rename( os.path.join( outdirpath, accession.upper() + '.fasta' ), os.path.join( outdirpath, accession.upper() + '_fasta' ) )
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34 printLog( outlogfile, '> FASTA file: \"' + accession.upper() + '.fasta\"' )
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35 accession_data = {
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36 'format': '.fasta',
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37 'filepath': os.path.join( outdirpath, accession.upper() + '.fasta' ),
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38 'filename': ''.join( c for c in accession.upper() if c in VALID_CHARS )
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39 }
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40 downloaded_files[ accession.upper() ] = accession_data
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41 return downloaded_files
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42
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43 # format = { fasta, fastq, accession }
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44 # this version skip the quality control procedure
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45 def createSBT( options, args ):
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46 outlogfile = str( options.outfile )
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47 outdirpath = str( options.outdir )
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48 if not outdirpath.endswith('/'): outdirpath += '/'
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49 if not os.path.exists( outdirpath ):
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50 os.mkdir( outdirpath )
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51 outdirpath = os.path.abspath( outdirpath )
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52 os.chdir( outdirpath )
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53 tooldirpath = os.path.abspath( str( options.tooldir ) )
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54 if not tooldirpath.endswith('/'): tooldirpath += '/'
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55
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56 formats = [ fo for fo in str( options.formats ).split( '|' ) if fo.strip() ]
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57 filepaths = [ filepath for filepath in str( options.filepaths ).split( '|' ) if filepath.strip() ]
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58 filenames = [ filename for filename in str( options.filenames ).split( '|' ) if filename.strip() ]
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59 compressed = [ True == int(c) for c in str( options.compressed ).split( '|' ) if c.strip() ]
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60 minabundances = [ int(minab) for minab in str( options.minabundances ).split( '|' ) if minab.strip() ]
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61 qualitythresholds = [ float(qthres) for qthres in str( options.qualitythresholds ).split( '|' ) if qthres.strip() ]
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62
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63 klen = int( options.klen )
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64 bfsize = int( options.bfsize )
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65
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66 if len(formats) == len(filepaths) == len(filenames) == len(compressed) == len(minabundances) == len(qualitythresholds):
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67 printLog( outlogfile, 'Retrieving experiments' )
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68 accessions = downloadAccessions( formats, filepaths, outlogfile, outdirpath )
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69 printLog( outlogfile, '> ' + str( len( accessions ) ) + ' experiments retrieved from the Sequence Read Archive' )
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70 acc_arr = [ a for a in accessions ]
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71 print str( acc_arr )
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72 if bfsize < 0: # estimate bloom filter size
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73 data_paths = ' '.join( accessions[ accession ][ 'filepath' ] for accession in accessions if 'filepath' in accessions[ accession ] )
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74 print data_paths
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75 if len( data_paths ) > 0:
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76 data_paths += ' '
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77 for dataset_idx in range(0, len(formats)):
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78 if formats[ dataset_idx ] != 'accessions':
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79 data_paths += ' '.join( path for path in filepaths[ dataset_idx ].split( ',' ) )
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80 # ntcard
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81 printLog( outlogfile, 'Estimating the Bloom Filter size with ntcard' )
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82 if len( data_paths ) > 0:
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83 ntcard_res_filepath = os.path.join( outdirpath, 'freq_k' + str( klen ) + '.hist' )
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84 ntcard_exitcode = os.system( 'ntcard --kmer=' + str( klen ) + ' ' + data_paths )
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85 print 'ntcard --kmer=' + str( klen ) + ' ' + data_paths
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86 if ntcard_exitcode > 0:
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87 printLog( outlogfile, '> [exitcode: ' + str(ntcard_exitcode) + '] an error with ntcard has occurred', exitcode=ERR_EXIT_CODE, exit=True )
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88 else:
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89 if os.path.exists( ntcard_res_filepath ):
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90 os.rename( ntcard_res_filepath, os.path.join( outdirpath, 'ntcard' + str( klen ) + '.txt' ) )
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91 ntcard_res_filepath = os.path.join( outdirpath, 'ntcard' + str( klen ) + '.txt' )
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92 var_F0 = None
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93 var_f1 = None
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94 with open( ntcard_res_filepath ) as ntcard_res:
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95 for line in ntcard_res:
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96 line = line.strip()
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97 if line:
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98 line_split = line.split( '\t' )
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99 if len(line_split) == 2:
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100 if line_split[0] == 'F0':
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101 var_F0 = int( line_split[1] )
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102 elif line_split[0] == 'f1':
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103 var_f1 = int( line_split[1] )
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104 if var_F0 is not None and var_f1 is not None:
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105 break
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106 if var_F0 is not None and var_f1 is not None:
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107 bfsize = var_F0 - var_f1
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108 printLog( outlogfile, '> estimated Bloom Filter size: ' + str(bfsize) )
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109 else:
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110 printLog( outlogfile, '> an error has occurred while estimating the Bloom Filter size', exitcode=ERR_EXIT_CODE, exit=True )
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111 else:
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112 printLog( outlogfile, '> an error with ntcard has occurred', exitcode=ERR_EXIT_CODE, exit=True )
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113 else:
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114 printLog( outlogfile, '> unable to estimate the Bloom Filter size', exitcode=ERR_EXIT_CODE, exit=True )
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115
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116 if bfsize > 0:
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117 for dataset_idx in range(0, len(formats)):
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118 if formats[ dataset_idx ] == 'accessions':
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119 with open( filepaths[ dataset_idx ] ) as accessions_file:
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120 for line in accessions_file:
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121 accession = line.split( '\t' )[0].strip().upper()
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122 if accession in accessions:
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123 curr_format = accessions[ accession ][ 'format' ]
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124 curr_compressed = 'uncompress'
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125 curr_filepath = accessions[ accession ][ 'filepath' ]
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126 curr_filename = accessions[ accession ][ 'filename' ]
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127 printLog( outlogfile, 'Processing \"' + accession + '\" ( format=\"' + curr_format +
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128 '\", compressed=\"' + str(False) + '\", fixed_name=\"' + curr_filename + '\" )' )
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129 print 'sh ' + tooldirpath + 'makebf.sh ' + curr_filepath + ' ' + curr_filename + ' ' + curr_format + ' ' + str(curr_compressed) + ' ' + outdirpath + ' ' + str( klen ) + ' ' + str( minabundances[ dataset_idx ] ) + ' ' + str( bfsize ) + ' 1 1'
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130 makebf_exitcode = os.system( 'sh ' + tooldirpath + 'makebf.sh ' + curr_filepath + ' ' + curr_filename + ' ' +
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131 curr_format + ' ' + str(curr_compressed) + ' ' + outdirpath + ' ' + str( klen ) + ' ' +
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132 str( minabundances[ dataset_idx ] ) + ' ' + str( bfsize ) + ' 1 1' )
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133 if makebf_exitcode > 0:
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134 printLog( outlogfile, '> [exitcode: ' + str(makebf_exitcode) + '] Bloom Filter file: FAILED ( \"' + accession + '\" will be excluded )' )
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135 else:
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136 printLog( outlogfile, '> Bloom Filter file: \"' + curr_filename + '.bf\"' )
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137 else:
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138 curr_format = '.' + formats[ dataset_idx ].lower()
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139 curr_compressed = '.gz' if compressed[ dataset_idx ] else 'uncompress'
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140 curr_filepaths = filepaths[ dataset_idx ].split( ',' )
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141 curr_filenames = filenames[ dataset_idx ].split( ',' )
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142 for curr_idx in range(0, len(curr_formats)):
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143 curr_filename_fixed = ''.join( c for c in curr_filenames[ curr_idx ] if c in VALID_CHARS )
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144 printLog( outlogfile, 'Processing \"' + curr_filenames[ curr_idx ] + '\" ( format=\"' + curr_format +
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145 '\", compressed=\"' + str(compressed[ dataset_idx ]) + '\", fixed_name=\"' + curr_filename_fixed + '\" )' )
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146 if compressed[ dataset_idx ]:
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147 makebf_exitcode = os.system( 'sh ' + tooldirpath + 'makebf.sh ' + curr_filepaths[ dataset_idx ] + ' ' + curr_filename_fixed + ' ' +
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148 curr_format + ' ' + str(curr_compressed) + ' ' + outdirpath + ' ' + str( klen ) + ' ' +
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149 str( minabundances[ dataset_idx ] ) + ' ' + str( bfsize ) + ' 0 1' )
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150 else:
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151 makebf_exitcode = os.system( 'sh ' + tooldirpath + 'makebf.sh ' + curr_filepaths[ dataset_idx ] + ' ' + curr_filename_fixed + ' ' +
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152 curr_format + ' ' + str(curr_compressed) + ' ' + outdirpath + ' ' + str( klen ) + ' ' +
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153 str( minabundances[ dataset_idx ] ) + ' ' + str( bfsize ) + ' 0 0' )
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154 if makebf_exitcode > 0:
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155 printLog( outlogfile, '> [exitcode: ' + str(makebf_exitcode) + '] Bloom Filter file: FAILED ( \"' + curr_filenames[ curr_idx ] + '\" will be excluded )' )
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156 else:
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157 printLog( outlogfile, '> Bloom Filter file: \"' + curr_filename_fixed + '.bf\"' )
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158 # Create a tree topology
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159 printLog( outlogfile, 'Creating a tree topology file' )
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160 bf_counter = len( glob.glob1( outdirpath, '*.bf' ) )
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161 if bf_counter > 0:
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162 cluster_exitcode = os.system( 'sh ' + tooldirpath + 'cluster.sh ' + outdirpath + ' ' + str( bfsize ) )
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163 if cluster_exitcode > 0:
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164 printLog( outlogfile, '> [exitcode: ' + str(cluster_exitcode) + '] an error has occurred during the creation of the topology file', exitcode=ERR_EXIT_CODE, exit=True )
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165 else:
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166 # Build the HowDeSBT nodes
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167 if os.path.exists( os.path.join( outdirpath, 'leafnames.txt' ) ):
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168 printLog( outlogfile, 'Building the Bloom Filter files for the tree' )
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169 build_exitcode = os.system( 'sh ' + tooldirpath + 'build.sh ' + outdirpath )
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170 if build_exitcode > 0:
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171 printLog( outlogfile, '> [exitcode: ' + str(build_exitcode) + '] an error has occurred during the creation of the Bloom Filter files for the tree', exitcode=ERR_EXIT_CODE, exit=True )
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172 else:
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173 printLog( outlogfile, '> the tree has been successfully built: \"howde.txt\"', exitcode=OK_EXIT_CODE, exit=True )
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174 '''
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175 howde_filepath = os.path.join( outdirpath, 'howde.txt' )
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176 howde_galaxy_filepath = os.path.join( outdirpath, 'howde_galaxy.txt' )
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177 howde_galaxy = open( howde_galaxy_filepath, 'w' )
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178 with open( howde_filepath ) as howde_file:
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179 for line in howde_file:
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180 line = line.strip()
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181 if line:
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182 # trim stars * and get node name
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183 # find galaxy file path to the node name
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184 # rewrite path with stars
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185 howde_galaxy.close()
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186 '''
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187 else:
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188 printLog( outlogfile, '> an error has occurred during the creation of the topology file', exitcode=ERR_EXIT_CODE, exit=True )
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189 else:
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190 printLog( outlogfile, '> no Bloom Filter files found', exitcode=ERR_EXIT_CODE, exit=True )
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191 else:
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192 printLog( outlogfile, '> ERROR: the Bloom Filter size is ' + str( bfsize ), exitcode=ERR_EXIT_CODE, exit=True )
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193 else:
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194 printLog( outlogfile, 'Something went wrong with the input parameters', exitcode=ERR_EXIT_CODE, exit=True )
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195
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196 def __main__():
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197 # Parse the command line options
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198 usage = ("Usage: create.py --formats file_formats --filepaths file_paths --filenames file_names "
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199 "--compressed file_compressed --minabundance min_abundance --qualitythresholds quality_thresholds "
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200 "--klen kmer_len --bfsize bloom_filter_size --outfile out_log_file_path --outdir out_dir_path")
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201 parser = optparse.OptionParser(usage = usage)
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202 parser.add_option("-v", "--version", action="store_true", dest="version",
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203 default=False, help="display version and exit")
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204 parser.add_option("-f", "--formats", type="string",
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205 action="store", dest="formats", help="list of file formats separated by a tab character")
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206 parser.add_option("-p", "--filepaths", type="string",
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207 action="store", dest="filepaths", help="list of input file paths separated by a tab character")
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208 parser.add_option("-n", "--filenames", type="string",
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209 action="store", dest="filenames", help="list of input file names separated by a tab character")
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210 parser.add_option("-c", "--compressed", type="string",
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211 action="store", dest="compressed", help="list of compressed flags related to the imput files separated by a tab character")
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212 parser.add_option("-m", "--minabundances", type="string",
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213 action="store", dest="minabundances", help="list of blooom filter minimum abundances related to the imput files separated by a tab character")
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214 parser.add_option("-q", "--qualitythresholds", type="string",
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215 action="store", dest="qualitythresholds", help="list of quality thresholds related to the imput files separated by a tab character")
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216 parser.add_option("-k", "--klen", type="int", default=21,
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217 action="store", dest="klen", help="k-mer length")
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218 parser.add_option("-b", "--bfsize", type="int", default=-1,
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219 action="store", dest="bfsize", help="bloom filter size")
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220 parser.add_option("-o", "--outfile", type="string", default="sbtres.txt",
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221 action="store", dest="outfile", help="output log file path")
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222 parser.add_option("-d", "--outdir", type="string", default="sbtres.txt",
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223 action="store", dest="outdir", help="output directory path")
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224 parser.add_option("-t", "--tooldir", type="string", default="./",
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225 action="store", dest="tooldir", help="tool directory path")
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226
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227 (options, args) = parser.parse_args()
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228 if options.version:
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229 print __version__
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230 else:
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231 createSBT( options, args )
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232
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233 if __name__ == "__main__": __main__()
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