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1 /*****************************************************************
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2 * SQUID - a library of functions for biological sequence analysis
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3 * Copyright (C) 1992-2002 Washington University School of Medicine
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4 *
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5 * This source code is freely distributed under the terms of the
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6 * GNU General Public License. See the files COPYRIGHT and LICENSE
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7 * for details.
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8 *****************************************************************/
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9
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10 /* revcomp.c
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11 *
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12 * Reverse complement of a IUPAC character string
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13 * RCS $Id: revcomp.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: revcomp.c,v 1.5 2002/06/25 20:06:06 eddy Exp)
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14 */
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15
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16 #include <stdio.h>
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17 #include <string.h>
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18 #include <ctype.h>
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19 #include "squid.h"
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20
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21 /* Function: revcomp()
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22 *
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23 * Purpose: Reverse complement seq; store in comp.
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24 * Can revcomp "in place" (revcomp(seq, seq)).
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25 *
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26 * Args: comp - destination for reverse complement of seq
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27 * seq - sequence to reverse complement
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28 *
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29 * Returns: NULL on failure; or a (useless) pointer to comp.
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30 */
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31 char *
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32 revcomp(char *comp, char *seq)
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33 {
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34 char *s;
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35 char c;
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36
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37 if (comp == NULL) return NULL;
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38 if (seq == NULL) return NULL;
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39
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40 StrReverse(comp, seq);
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41 for (s = comp; *s != '\0'; s++)
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42 {
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43 c = *s;
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44 c = sre_toupper(c);
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45 switch (c) {
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46 case 'A': c = 'T'; break;
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47 case 'C': c = 'G'; break;
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48 case 'G': c = 'C'; break;
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49 case 'T': c = 'A'; break;
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50 case 'U': c = 'A'; break;
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51 case 'R': c = 'Y'; break;
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52 case 'Y': c = 'R'; break;
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53 case 'M': c = 'K'; break;
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54 case 'K': c = 'M'; break;
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55 case 'S': c = 'S'; break;
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56 case 'W': c = 'W'; break;
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57 case 'H': c = 'D'; break;
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58 case 'D': c = 'H'; break;
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59 case 'B': c = 'V'; break;
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60 case 'V': c = 'B'; break;
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61 default: break; /* anything else? leave it; it's prob a gap or an X */
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62 }
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63 if (islower((int) *s)) c = (char) sre_tolower((int) c);
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64 *s = c;
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65 }
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66 return comp;
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67 }
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68
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69 #ifdef REVCOMP_TESTDRIVER
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70 /* gcc -g -DREVCOMP_TESTDRIVER revcomp.c sre_string.c shuffle.c sre_math.c sre_ctype.c sqerror.c -lm
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71 */
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72 int
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73 main(void)
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74 {
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75 float p[4] = {0.25, 0.25, 0.25, 0.25};
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76 char *alphabet = "ACGT";
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77 int len = 10;
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78 char *seq;
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79
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80 seq = RandomSequence(alphabet, p, 4, len);
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81 printf("%s\n", seq);
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82 revcomp(seq, seq);
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83 printf("%s\n", seq);
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84 free(seq);
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85 exit(0);
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86 }
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87 #endif
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