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1 #!/usr/bin/env python
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2 """
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3 #
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4 #------------------------------------------------------------------------------
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5 # University of Minnesota
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6 # Copyright 2013, Regents of the University of Minnesota
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7 #------------------------------------------------------------------------------
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8 # Author:
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9 #
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10 # James E Johnson
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11 #
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12 #------------------------------------------------------------------------------
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13 """
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14
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15 """
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16 Takes 2 tabular files as input:
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17 1. The file to be filtered
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18 2. The reference file
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19
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20 The string value of selected column of the input file is searched for
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21 in the string values of the selected column of the reference file.
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22
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23 The intended purpose is to filter a peptide fasta file in tabular format
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24 by whether those peptide sequences are found in a reference fasta file.
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25
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26 """
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27 import sys,re,os.path
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28 import tempfile
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29 import optparse
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30 from optparse import OptionParser
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31 import logging
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32
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33
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34 def __main__():
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35 #Parse Command Line
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36 parser = optparse.OptionParser()
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37 parser.add_option( '-i', '--input', dest='input', help='The input file to filter. (Otherwise read from stdin)' )
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38 parser.add_option( '-r', '--reference', dest='reference', help='The reference file to filter against' )
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39 parser.add_option( '-o', '--output', dest='output', help='The output file for input lines filtered by reference')
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40 parser.add_option( '-f', '--filtered', dest='filtered', help='The output file for input lines not in the output')
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41 parser.add_option('-c','--input_column', dest='input_column', default=None, help='The column for the value in the input file. (first column = 1, default to last column)')
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42 parser.add_option('-C','--reference_column', dest='reference_column', default=None, help='The column for the value in the reference file. (first column = 1, default to last column)')
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43 parser.add_option( '-I', '--case_insensitive', dest='ignore_case', action="store_true", default=False, help='case insensitive' )
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44 parser.add_option( '-k', '--keep', dest='keep', action="store_true", default=False, help='' )
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45 parser.add_option( '-a', '--annotation_columns', dest='annotation_columns', default=None, help='If string is found, add these columns from reference' )
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46 parser.add_option( '-s', '--annotation_separator', dest='annotation_separator', default=';', help='separator character between annotations from different lines' )
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47 parser.add_option( '-S', '--annotation_col_sep', dest='annotation_col_sep', default=',', help='separator character between annotation column from the same line' )
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48 parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout' )
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49 (options, args) = parser.parse_args()
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50 # Input files
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51 if options.input != None:
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52 try:
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53 inputPath = os.path.abspath(options.input)
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54 inputFile = open(inputPath, 'r')
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55 except Exception, e:
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56 print >> sys.stderr, "failed: %s" % e
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57 exit(2)
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58 else:
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59 inputFile = sys.stdin
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60 # Reference
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61 if options.reference == None:
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62 print >> sys.stderr, "failed: reference file is required"
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63 exit(2)
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64 # Output files
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65 outFile = None
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66 filteredFile = None
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67 if options.filtered == None and options.output == None:
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68 #write to stdout
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69 outFile = sys.stdout
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70 else:
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71 if options.output != None:
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72 try:
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73 outPath = os.path.abspath(options.output)
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74 outFile = open(outPath, 'w')
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75 except Exception, e:
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76 print >> sys.stderr, "failed: %s" % e
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77 exit(3)
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78 if options.filtered != None:
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79 try:
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80 filteredPath = os.path.abspath(options.filtered)
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81 filteredFile = open(filteredPath, 'w')
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82 except Exception, e:
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83 print >> sys.stderr, "failed: %s" % e
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84 exit(3)
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85 incol = -1
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86 if options.input_column and options.input_column > 0:
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87 incol = int(options.input_column)-1
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88 refcol = -1
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89 if options.reference_column and options.reference_column > 0:
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90 refcol = int(options.reference_column)-1
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91 if options.annotation_columns:
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92 annotate = True
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93 annotation_columns = [int(x) - 1 for x in options.annotation_columns.split(',')]
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94 else:
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95 annotate = False
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96 refFile = None
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97 num_found = 0
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98 num_novel = 0
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99 for ln,line in enumerate(inputFile):
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100 annotations = []
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101 try:
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102 found = False
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103 search_string = line.split('\t')[incol].rstrip('\r\n')
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104 if options.ignore_case:
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105 search_string = search_string.upper()
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106 if options.debug:
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107 print >> sys.stderr, "search: %s" % (search_string)
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108 refFile = open(options.reference,'r')
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109 for tn,fline in enumerate(refFile):
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110 fields = fline.split('\t')
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111 target_string =fields[refcol]
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112 if options.ignore_case:
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113 target_string = target_string.upper()
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114 if options.debug:
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115 print >> sys.stderr, "in: %s %s %s" % (search_string,search_string in target_string,target_string)
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116 if search_string in target_string:
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117 found = True
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118 if annotate:
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119 annotation = options.annotation_col_sep.join([fields[i] for i in annotation_columns])
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120 annotations.append(annotation)
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121 else:
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122 break
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123 if found:
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124 num_found += 1
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125 if annotate:
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126 line = '%s\t%s\n' % (line.rstrip('\r\n'),options.annotation_separator.join(annotations))
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127 if options.keep == True:
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128 if outFile:
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129 outFile.write(line)
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130 else:
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131 if filteredFile:
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132 filteredFile.write(line)
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133 else:
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134 num_novel += 1
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135 if options.keep == True:
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136 if filteredFile:
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137 filteredFile.write(line)
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138 else:
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139 if outFile:
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140 outFile.write(line)
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141 except Exception, e:
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142 print >> sys.stderr, "failed: Error reading %s - %s" % (options.reference,e)
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143 finally:
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144 if refFile:
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145 refFile.close()
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146 print >> sys.stdout, "found: %d novel: %d" % (num_found,num_novel)
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147
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148 if __name__ == "__main__" : __main__()
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149
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