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19
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1 #!/usr/bin/env python
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2
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3 import sys, os, optparse, shutil
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4
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5 __version__ = "1.0.0"
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6 VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
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7 # in the case of collections, exitcodes equal to 0 and 1 are not considered errors
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8 ERR_EXIT_CODE = 2
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9 OK_EXIT_CODE = 0
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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 querySBT( options, args ):
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19 output_dir_path = options.outputdir
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20 outlogfile = options.outfile
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21
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22 tree_file_paths = options.treep.split( ',' )
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23 tree_file_names = options.treen.split( ',' )
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24 tree_def_filepath = None
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25 leafnames_filepath = None
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26 for idx, tree_file_name in enumerate( tree_file_names ):
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27 if tree_file_name == 'howde':
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28 tree_def_filepath = tree_file_paths[ idx ]
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29 elif tree_file_name == 'leafnames':
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30 leafnames_filepath = tree_file_paths[ idx ]
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31 if tree_def_filepath is not None and leafnames_filepath is not None:
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32 break
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33
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34 if tree_def_filepath is not None and leafnames_filepath is not None:
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35 leafnames_counter = 0
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36 with open( leafnames_filepath ) as leafnames_file:
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37 for line in leafnames_file:
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38 if line.strip():
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39 leafnames_counter += 1
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40 if leafnames_counter > 0:
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41 printLog( outlogfile, 'The selected collection contains a valid tree' )
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42 shutil.copyfile( tree_def_filepath, 'howde.txt' )
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43 tree_def_filepath = 'howde.txt'
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44 for idx, tree_file_name in enumerate( tree_file_names ):
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45 if tree_file_name.endswith( 'detbrief.rrr' ):
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46 shutil.copyfile( tree_file_paths[ idx ], tree_file_name + '.bf' )
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47
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48 printLog( outlogfile, 'Creating batch of queries' )
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49 # create tmp batch file
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50 batch_file_name = 'queries.fa'
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51 batch_file = open( batch_file_name, 'w' )
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52
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53 comma_sep_file_paths = options.files
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54 # check if options.files contains at least one file path
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55 if comma_sep_file_paths is not None:
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56 # split file paths
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57 file_paths = comma_sep_file_paths.split(",")
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58 # split file names
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59 file_names = options.names.split(",")
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60 for idx, file_path in enumerate(file_paths):
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61 fixed_file_name = ''.join( c for c in file_names[ idx ] if c in VALID_CHARS )
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62 printLog( outlogfile, '> processing file ' + file_names[ idx ] + ' ( fixed_name=\"' + fixed_file_name + '\" ) ' )
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63 with open(file_path, 'r') as content_file:
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64 for line in content_file:
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65 line = line.strip()
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66 if line:
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67 line_split = line.strip().split("\t") # split on tab
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68 if len(line_split) == 2: # 0:id , 1:seq , otherwise skip line
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69 original_seq_id = line_split[0]
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70 # fix seq_id using valid chars only
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71 seq_id = ''.join( c for c in original_seq_id if c in VALID_CHARS )
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72 printLog( outlogfile, '> sequence ' + original_seq_id + ' ( fixed_name=\"' + seq_id + '\" )' )
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73 seq_text = line_split[1]
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74
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75 # write on batch file
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76 batch_file.write( '> ' + fixed_file_name + '_' + seq_id + '\n' + seq_text + '\n' )
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77 batch_file.close()
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78 # query the tree
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79 printLog( outlogfile, 'Querying the tree' )
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80 query_res_file_path = os.path.abspath( 'answer.txt' )
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81 sort_param = '--sort'
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82 if options.sort == 0:
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83 sort_param = ''
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84 query_exitcode = os.system( 'howdesbt query --tree=' + os.path.abspath( tree_def_filepath ) + ' ' + os.path.abspath( batch_file_name ) + '=' + str(options.threshold) + ' --out=' + query_res_file_path ) + ' ' + sort_param
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85 if query_exitcode > 0:
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86 printLog( outlogfile, '> ERROR: an error has occurred while querying the tree with the sequence [id: ' + seq_id + '] in input file ' + file_names[ idx ] )
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87 else:
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88 if os.path.exists( query_res_file_path ):
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89 with open( query_res_file_path ) as query_res_file:
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90 file_path = ''
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91 theta_matches = 0
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92 for line in query_res_file:
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93 line = line.strip()
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94 if line:
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95 if line.startswith( '*' ):
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96 line_split = line.split( ' ' )
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97 theta_matches = int( line_split[ 1 ] )
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98 file_name = line_split[ 0 ].replace( '*', '' )
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99 file_path = os.path.join( output_dir_path, file_name + '_txt' )
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100 open( file_path, 'a' ).close()
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101 else:
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102 res_file = open( file_path, 'a+' )
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103 fraction = str( theta_matches ) + '/' + str( leafnames_counter )
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104 score = format( round( float( theta_matches ) / float( leafnames_counter ) , 6 ), '6f' )
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105 res_file.write( line + '\t' + fraction + '\t' + score + '\n' )
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106 res_file.close()
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107 else:
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108 printLog( outlogfile, 'An error has occurred while querying the tree', exitcode=ERR_EXIT_CODE, exit=True )
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109 else:
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110 printLog( outlogfile, 'The selected collection does not contain a valid tree', exitcode=ERR_EXIT_CODE, exit=True )
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111 else:
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112 printLog( outlogfile, 'The selected collection does not contain a valid tree', exitcode=ERR_EXIT_CODE, exit=True )
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113
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114 def __main__():
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115 # Parse the command line options
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116 usage = "Usage: query.py --files comma_sep_file_paths --names comma_seq_file_names --sequences sequences_text --search search_mode --exact exact_alg --sthreshold threshold --outputdir output_dir_path"
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117 parser = optparse.OptionParser(usage = usage)
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118 parser.add_option("-v", "--version", action="store_true", dest="version",
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119 default=False, help="display version and exit")
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120 parser.add_option("-f", "--files", type="string",
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121 action="store", dest="files", help="comma separated files path")
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122 parser.add_option("-n", "--names", type="string",
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123 action="store", dest="names", help="comma separated names associated to the files specified in --files")
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124 parser.add_option("-k", "--treep", type="string",
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125 action="store", dest="treep", help="paths of files in collection")
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126 parser.add_option("-m", "--treen", type="string",
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127 action="store", dest="treen", help="names of files in collection")
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128 parser.add_option("-t", "--threshold", type="float", default=0.7,
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129 action="store", dest="threshold", help="search threshold")
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130 parser.add_option("-s", "--sort", type="int", default=1,
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131 action="store", dest="sort", help="sort results")
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132 parser.add_option("-o", "--outputdir", type="string", default="output",
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133 action="store", dest="outputdir", help="output directory (collection) path")
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134 parser.add_option("-r", "--outfile", type="string", default="query.txt",
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135 action="store", dest="outfile", help="output log file path")
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136
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137 (options, args) = parser.parse_args()
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138 if options.version:
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139 print __version__
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140 else:
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141 # create output dir (collection)
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142 output_dir_path = options.outputdir
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143 if not os.path.exists(output_dir_path):
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144 os.makedirs(output_dir_path)
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145
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146 querySBT( options, args )
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147
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148 if __name__ == "__main__": __main__()
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