Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/progs/srf2fasta.c @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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rev | line source |
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0
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 /* |
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2 * ====================================================================== |
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3 * This software has been created by Genome Research Limited (GRL). |
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4 * |
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5 * GRL hereby grants permission to use, copy, modify and distribute |
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6 * this software and its documentation for non-commercial purposes |
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7 * without fee at the user's own risk on the basis set out below. |
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8 * |
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9 * GRL neither undertakes nor accepts any duty whether contractual or |
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10 * otherwise in connection with the software, its use or the use of |
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11 * any derivative, and makes no representations or warranties, express |
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12 * or implied, concerning the software, its suitability, fitness for |
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13 * a particular purpose or non-infringement. |
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14 * |
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15 * In no event shall the authors of the software or GRL be responsible |
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16 * or liable for any loss or damage whatsoever arising in any way |
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17 * directly or indirectly out of the use of this software or its |
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18 * derivatives, even if advised of the possibility of such damage. |
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19 * |
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20 * Our software can be freely distributed under the conditions set out |
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21 * above, and must contain this copyright notice. |
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22 * ====================================================================== |
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23 */ |
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24 |
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25 /* |
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26 * This performs a linear (non-indexed) search for a trace in an SRF archive. |
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27 * |
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28 * It's not intended as a suitable production program or as a library of code |
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29 * to use, but as a test and benchmark statistic. |
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30 */ |
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31 |
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32 #include <stdio.h> |
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33 #include <math.h> |
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34 #include <string.h> |
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35 #include <fcntl.h> |
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36 |
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37 #include <io_lib/Read.h> |
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38 #include <io_lib/misc.h> |
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39 #include <io_lib/ztr.h> |
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40 #include <io_lib/srf.h> |
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41 |
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42 /* ------------------------------------------------------------------------ */ |
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43 |
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44 #define MAX_READ_LEN 10000 |
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45 void ztr2fasta(ztr_t *z, char *name) { |
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46 int i, nc; |
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47 char buf[MAX_READ_LEN*2 + 512 + 6]; |
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48 char *seq = buf; |
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49 ztr_chunk_t **chunks; |
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50 |
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51 /* Extract the sequence only */ |
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52 chunks = ztr_find_chunks(z, ZTR_TYPE_BASE, &nc); |
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53 if (nc != 1) { |
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54 fprintf(stderr, "Zero or greater than one BASE chunks found.\n"); |
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55 if (chunks) |
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56 free(chunks); |
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57 return; |
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58 } |
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59 |
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60 uncompress_chunk(z, chunks[0]); |
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61 |
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62 /* Construct fasta entry */ |
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63 *seq++ = '>'; |
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64 while (*name) |
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65 *seq++ = *name++; |
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66 *seq++ = '\n'; |
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67 |
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68 for (i = 1; i < chunks[0]->dlength; i++) { |
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69 char base = chunks[0]->data[i]; |
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70 switch (base) { |
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71 case 'A': case 'a': |
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72 case 'C': case 'c': |
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73 case 'G': case 'g': |
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74 case 'T': case 't': |
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75 *seq++ = base; |
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76 break; |
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77 default: |
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78 *seq++ = 'N'; |
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79 } |
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80 } |
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81 *seq++ = '\n'; |
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82 |
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83 fwrite(buf, 1, seq - buf, stdout); |
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84 free(chunks); |
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85 |
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86 return; |
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87 } |
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88 |
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89 /* ------------------------------------------------------------------------ */ |
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90 void usage(void) { |
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91 fprintf(stderr, "Usage: srf2fasta [-C] archive_name\n"); |
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92 exit(1); |
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93 } |
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94 |
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95 int main(int argc, char **argv) { |
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96 char *ar_name; |
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97 srf_t *srf; |
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98 char name[512]; |
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99 ztr_t *ztr; |
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100 int mask = 0, i; |
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101 |
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102 /* Parse args */ |
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103 for (i = 1; i < argc && argv[i][0] == '-'; i++) { |
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104 if (!strcmp(argv[i], "-")) { |
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105 break; |
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106 } else if (!strcmp(argv[i], "-C")) { |
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107 mask = SRF_READ_FLAG_BAD_MASK; |
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108 } else { |
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109 usage(); |
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110 } |
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111 } |
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112 |
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113 if (i == argc) { |
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114 usage(); |
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115 } |
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116 ar_name = argv[i]; |
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117 |
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118 if (NULL == (srf = srf_open(ar_name, "r"))) { |
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119 perror(ar_name); |
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120 return 4; |
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121 } |
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122 |
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123 read_sections(READ_BASES); |
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124 |
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125 #ifdef _WIN32 |
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126 _setmode(_fileno(stdout), _O_BINARY); |
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127 #endif |
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128 |
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129 while (NULL != (ztr = srf_next_ztr(srf, name, mask))) { |
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130 ztr2fasta(ztr, name); |
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131 delete_ztr(ztr); |
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132 } |
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133 |
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134 srf_destroy(srf, 1); |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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135 |
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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136 return 0; |
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137 } |