|
3
|
1 /*
|
|
|
2 FASTX-toolkit - FASTA/FASTQ preprocessing tools.
|
|
|
3 Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
|
|
|
4
|
|
|
5 This program is free software: you can redistribute it and/or modify
|
|
|
6 it under the terms of the GNU Affero General Public License as
|
|
|
7 published by the Free Software Foundation, either version 3 of the
|
|
|
8 License, or (at your option) any later version.
|
|
|
9
|
|
|
10 This program is distributed in the hope that it will be useful,
|
|
|
11 but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
|
12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
|
13 GNU Affero General Public License for more details.
|
|
|
14
|
|
|
15 You should have received a copy of the GNU Affero General Public License
|
|
|
16 along with this program. If not, see <http://www.gnu.org/licenses/>.
|
|
|
17 */
|
|
|
18 #include <limits.h>
|
|
|
19 #include <stdio.h>
|
|
|
20 #include <stdlib.h>
|
|
|
21 #include <string.h>
|
|
|
22 #include <getopt.h>
|
|
|
23 #include <errno.h>
|
|
|
24 #include <err.h>
|
|
|
25
|
|
|
26 #include <config.h>
|
|
|
27
|
|
|
28 #include "fastx.h"
|
|
|
29 #include "fastx_args.h"
|
|
|
30
|
|
|
31 #define MAX_ADAPTER_LEN 100
|
|
|
32
|
|
|
33 const char* usage=
|
|
|
34 "usage: fastx_artifacts_filter [-h] [-v] [-z] [-i INFILE] [-o OUTFILE]\n" \
|
|
|
35 "\n" \
|
|
|
36 "version " VERSION "\n" \
|
|
|
37 " [-h] = This helpful help screen.\n" \
|
|
|
38 " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \
|
|
|
39 " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \
|
|
|
40 " [-z] = Compress output with GZIP.\n" \
|
|
|
41 " [-v] = Verbose - report number of processed reads.\n" \
|
|
|
42 " If [-o] is specified, report will be printed to STDOUT.\n" \
|
|
|
43 " If [-o] is not specified (and output goes to STDOUT),\n" \
|
|
|
44 " report will be printed to STDERR.\n" \
|
|
|
45 "\n";
|
|
|
46
|
|
|
47 #define DO_NOT_TRIM_LAST_BASE (0)
|
|
|
48
|
|
|
49 FASTX fastx;
|
|
|
50
|
|
|
51 int parse_commandline(int argc, char* argv[])
|
|
|
52 {
|
|
|
53 return fastx_parse_cmdline(argc, argv, "", NULL);
|
|
|
54 }
|
|
|
55
|
|
|
56 int artifact_sequence(const FASTX *fastx)
|
|
|
57 {
|
|
|
58 int n_count=0;
|
|
|
59 int a_count=0;
|
|
|
60 int c_count=0;
|
|
|
61 int t_count=0;
|
|
|
62 int g_count=0;
|
|
|
63 int total_count=0;
|
|
|
64
|
|
|
65 int max_allowed_different_bases = 3 ;
|
|
|
66
|
|
|
67 int i=0;
|
|
|
68
|
|
|
69 while (1) {
|
|
|
70 if (fastx->nucleotides[i]==0)
|
|
|
71 break;
|
|
|
72
|
|
|
73 total_count++;
|
|
|
74 switch(fastx->nucleotides[i])
|
|
|
75 {
|
|
|
76 case 'A':
|
|
|
77 a_count++;
|
|
|
78 break;
|
|
|
79 case 'C':
|
|
|
80 c_count++;
|
|
|
81 break;
|
|
|
82 case 'G':
|
|
|
83 g_count++;
|
|
|
84 break;
|
|
|
85 case 'T':
|
|
|
86 t_count++;
|
|
|
87 break;
|
|
|
88 case 'N':
|
|
|
89 n_count++;
|
|
|
90 break;
|
|
|
91 default:
|
|
|
92 errx(1, __FILE__":%d: invalid nucleotide value (%c) at position %d",
|
|
|
93 __LINE__, fastx->nucleotides[i], i ) ;
|
|
|
94 }
|
|
|
95 i++;
|
|
|
96 }
|
|
|
97
|
|
|
98 //Rules for artifacts
|
|
|
99
|
|
|
100 if ( a_count>=(total_count-max_allowed_different_bases)
|
|
|
101 ||
|
|
|
102 c_count>=(total_count-max_allowed_different_bases)
|
|
|
103 ||
|
|
|
104 g_count>=(total_count-max_allowed_different_bases)
|
|
|
105 ||
|
|
|
106 t_count>=(total_count-max_allowed_different_bases)
|
|
|
107 )
|
|
|
108 return 1;
|
|
|
109
|
|
|
110
|
|
|
111 return 0;
|
|
|
112 }
|
|
|
113
|
|
|
114 int main(int argc, char* argv[])
|
|
|
115 {
|
|
|
116 parse_commandline(argc, argv);
|
|
|
117
|
|
|
118 fastx_init_reader(&fastx, get_input_filename(),
|
|
|
119 FASTA_OR_FASTQ, ALLOW_N, REQUIRE_UPPERCASE);
|
|
|
120
|
|
|
121 fastx_init_writer(&fastx, get_output_filename(),
|
|
|
122 OUTPUT_SAME_AS_INPUT, compress_output_flag());
|
|
|
123
|
|
|
124 while ( fastx_read_next_record(&fastx) ) {
|
|
|
125
|
|
|
126 if ( artifact_sequence(&fastx) ) {
|
|
|
127 } else {
|
|
|
128 fastx_write_record(&fastx);
|
|
|
129 }
|
|
|
130 }
|
|
|
131
|
|
|
132 //Print verbose report
|
|
|
133 if ( verbose_flag() ) {
|
|
|
134 fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ;
|
|
|
135 fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ;
|
|
|
136
|
|
|
137 size_t discarded = num_input_reads(&fastx) - num_output_reads(&fastx) ;
|
|
|
138 fprintf(get_report_file(), "discarded %zu (%zu%%) artifact reads.\n",
|
|
|
139 discarded, (discarded*100)/( num_input_reads(&fastx) ) ) ;
|
|
|
140 }
|
|
|
141
|
|
|
142 return 0;
|
|
|
143 }
|
