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| 1 | +#!/usr/bin/env python3 |
| 2 | + |
| 3 | + |
| 4 | +import os.path |
| 5 | +import sys |
| 6 | +import optparse |
| 7 | + |
| 8 | + |
| 9 | +""" |
| 10 | +# |
| 11 | +#------------------------------------------------------------------------------ |
| 12 | +# University of Minnesota |
| 13 | +# Copyright 2013, Regents of the University of Minnesota |
| 14 | +#------------------------------------------------------------------------------ |
| 15 | +# Author: |
| 16 | +# |
| 17 | +# James E Johnson |
| 18 | +# |
| 19 | +#------------------------------------------------------------------------------ |
| 20 | +""" |
| 21 | + |
| 22 | +""" |
| 23 | +Takes 2 tabular files as input: |
| 24 | + 1. The file to be filtered |
| 25 | + 2. The reference file |
| 26 | +
|
| 27 | +The string value of selected column of the input file is searched for |
| 28 | +in the string values of the selected column of the reference file. |
| 29 | +
|
| 30 | +The intended purpose is to filter a peptide fasta file in tabular format |
| 31 | +by whether those peptide sequences are found in a reference fasta file. |
| 32 | +
|
| 33 | +""" |
| 34 | + |
| 35 | + |
| 36 | +def __main__(): |
| 37 | + # Parse Command Line |
| 38 | + parser = optparse.OptionParser() |
| 39 | + parser.add_option('-i', '--input', dest='input', help='The input file to filter. (Otherwise read from stdin)') |
| 40 | + parser.add_option('-r', '--reference', dest='reference', help='The reference file to filter against') |
| 41 | + parser.add_option('-o', '--output', dest='output', help='The output file for input lines filtered by reference') |
| 42 | + parser.add_option('-f', '--filtered', dest='filtered', help='The output file for input lines not in the output') |
| 43 | + parser.add_option('-c', '--input_column', dest='input_column', type="int", default=None, help='The column for the value in the input file. (first column = 1, default to last column)') |
| 44 | + parser.add_option('-C', '--reference_column', dest='reference_column', type="int", default=None, help='The column for the value in the reference file. (first column = 1, default to last column)') |
| 45 | + parser.add_option('-I', '--case_insensitive', dest='ignore_case', action="store_true", default=False, help='case insensitive') |
| 46 | + parser.add_option('-R', '--reverse_find', dest='reverse_find', action="store_true", default=False, help='find the reference string in the input string') |
| 47 | + parser.add_option('-B', '--test_reverse', dest='test_reverse', action="store_true", default=False, help='Also search for reversed input string in reference') |
| 48 | + parser.add_option('-D', '--test_dna_reverse_complement', dest='test_reverse_comp', action="store_true", default=False, help='Also search for the DNA reverse complement of input string') |
| 49 | + parser.add_option('-k', '--keep', dest='keep', action="store_true", default=False, help='') |
| 50 | + parser.add_option('-a', '--annotation_columns', dest='annotation_columns', default=None, help='If string is found, add these columns from reference') |
| 51 | + parser.add_option('-s', '--annotation_separator', dest='annotation_separator', default=';', help='separator character between annotations from different lines') |
| 52 | + parser.add_option('-S', '--annotation_col_sep', dest='annotation_col_sep', default=', ', help='separator character between annotation column from the same line') |
| 53 | + parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout') |
| 54 | + (options, args) = parser.parse_args() |
| 55 | + |
| 56 | + # revcompl = lambda x: ''.join([{'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'a': 't', 'c': 'g', 'g': 'c', 't': 'a', 'N': 'N', 'n': 'n'}[B] for B in x][: : -1]) |
| 57 | + |
| 58 | + COMP = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'a': 't', 'c': 'g', 'g': 'c', 't': 'a', 'N': 'N', 'n': 'n'} |
| 59 | + |
| 60 | + def revcompl(seq): |
| 61 | + return ''.join([COMP[B] for B in seq][::-1]) |
| 62 | + |
| 63 | + def test_rcomplement(seq, target): |
| 64 | + if options.test_reverse_comp: |
| 65 | + try: |
| 66 | + comp = revcompl(seq) |
| 67 | + return comp in target |
| 68 | + except Exception: |
| 69 | + pass |
| 70 | + return False |
| 71 | + |
| 72 | + def test_reverse(seq, target): |
| 73 | + return options.test_reverse and seq and seq[::-1] in target |
| 74 | + |
| 75 | + # Input files |
| 76 | + if options.input is not None: |
| 77 | + try: |
| 78 | + inputPath = os.path.abspath(options.input) |
| 79 | + inputFile = open(inputPath, 'r') |
| 80 | + except Exception as e: |
| 81 | + print("failed: %s" % e, file=sys.stderr) |
| 82 | + exit(2) |
| 83 | + else: |
| 84 | + inputFile = sys.stdin |
| 85 | + # Reference |
| 86 | + if options.reference is None: |
| 87 | + print("failed: reference file is required", file=sys.stderr) |
| 88 | + exit(2) |
| 89 | + # Output files |
| 90 | + outFile = None |
| 91 | + filteredFile = None |
| 92 | + if options.filtered is None and options.output is None: |
| 93 | + # write to stdout |
| 94 | + outFile = sys.stdout |
| 95 | + else: |
| 96 | + if options.output is not None: |
| 97 | + try: |
| 98 | + outPath = os.path.abspath(options.output) |
| 99 | + outFile = open(outPath, 'w') |
| 100 | + except Exception as e: |
| 101 | + print("failed: %s" % e, file=sys.stderr) |
| 102 | + exit(3) |
| 103 | + if options.filtered is not None: |
| 104 | + try: |
| 105 | + filteredPath = os.path.abspath(options.filtered) |
| 106 | + filteredFile = open(filteredPath, 'w') |
| 107 | + except Exception as e: |
| 108 | + print("failed: %s" % e, file=sys.stderr) |
| 109 | + exit(3) |
| 110 | + incol = -1 |
| 111 | + if options.input_column and options.input_column > 0: |
| 112 | + incol = int(options.input_column)-1 |
| 113 | + refcol = -1 |
| 114 | + if options.reference_column and options.reference_column > 0: |
| 115 | + refcol = int(options.reference_column)-1 |
| 116 | + if options.annotation_columns: |
| 117 | + annotate = True |
| 118 | + annotation_columns = [int(x) - 1 for x in options.annotation_columns.split(', ')] |
| 119 | + else: |
| 120 | + annotate = False |
| 121 | + refFile = None |
| 122 | + num_found = 0 |
| 123 | + num_novel = 0 |
| 124 | + for ln, line in enumerate(inputFile): |
| 125 | + annotations = [] |
| 126 | + try: |
| 127 | + found = False |
| 128 | + search_string = line.split('\t')[incol].rstrip('\r\n') |
| 129 | + if options.ignore_case: |
| 130 | + search_string = search_string.upper() |
| 131 | + if options.debug: |
| 132 | + print("search: %s" % (search_string), file=sys.stderr) |
| 133 | + refFile = open(options.reference, 'r') |
| 134 | + for tn, fline in enumerate(refFile): |
| 135 | + fields = fline.split('\t') |
| 136 | + target_string = fields[refcol].rstrip('\r\n') |
| 137 | + if options.ignore_case: |
| 138 | + target_string = target_string.upper() |
| 139 | + search = search_string if not options.reverse_find else target_string |
| 140 | + target = target_string if not options.reverse_find else search_string |
| 141 | + if options.debug: |
| 142 | + print("in: %s %s %s" % (search, search in target, target), file=sys.stderr) |
| 143 | + if search in target or test_reverse(search, target) or test_rcomplement(search, target): |
| 144 | + found = True |
| 145 | + if annotate: |
| 146 | + annotation = options.annotation_col_sep.join([fields[i] for i in annotation_columns]) |
| 147 | + annotations.append(annotation) |
| 148 | + else: |
| 149 | + break |
| 150 | + if found: |
| 151 | + num_found += 1 |
| 152 | + if annotate: |
| 153 | + line = '%s\t%s\n' % (line.rstrip('\r\n'), options.annotation_separator.join(annotations)) |
| 154 | + if options.keep is True: |
| 155 | + if outFile: |
| 156 | + outFile.write(line) |
| 157 | + else: |
| 158 | + if filteredFile: |
| 159 | + filteredFile.write(line) |
| 160 | + else: |
| 161 | + num_novel += 1 |
| 162 | + if options.keep is True: |
| 163 | + if filteredFile: |
| 164 | + filteredFile.write(line) |
| 165 | + else: |
| 166 | + if outFile: |
| 167 | + outFile.write(line) |
| 168 | + except Exception as e: |
| 169 | + print("failed: Error reading %s - %s" % (options.reference, e), file=sys.stderr) |
| 170 | + finally: |
| 171 | + if refFile: |
| 172 | + refFile.close() |
| 173 | + print("found: %d novel: %d" % (num_found, num_novel), file=sys.stdout) |
| 174 | + |
| 175 | + |
| 176 | +if __name__ == "__main__": |
| 177 | + __main__() |
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