website/archive/binaries/mac/src/fasta34/faatran.c

   1
   2 /* copyright (c) 1996, 1997, 1998, 1999 William R. Pearson and the
   3    U. of Virginia */
   4
   5 /* $Name: fa_34_26_5 $ - $Id: faatran.c,v 1.6 2007/04/02 18:08:11 wrp Exp $ */
   6
   7 /*      aatran.c        translates from nt to aa, 1 char codes */
   8 /*      modified July 2, 1987 for all 6 frames */
   9 /*      23 Jan 1991     fixed bug for short sequences */
  10
  11 /*      this mapping is not alphabet independent */
  12
  13 #define XTERNAL
  14 #include <stdio.h>
  15 #include <stdlib.h>
  16
  17 #include "upam.h"
  18 #include "uascii.h"
  19
  20 /*
  21 1. The Standard Code (transl_table=1)
  22
  23 By default all transl_table in GenBank flatfiles are equal to id 1, and this
  24 is not shown. When transl_table is not equal to id 1, it is shown as a
  25 qualifier on the CDS feature.
  26
  27 */
  28 static
  29 char *AA1="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
  30 /*
  31   Starts = ---M---------------M---------------M----------------------------
  32   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  33   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  34   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
  35
  36 2. The Vertebrate Mitochondrial Code (transl_table=2)
  37 */
  38 static
  39 char *AA2 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG";
  40 /*
  41   Starts = --------------------------------MMMM---------------M------------
  42   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  43   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  44   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
  45
  46 3. The Yeast Mitochondrial Code (transl_table=3)
  47 */
  48 static
  49 char *AA3 ="FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
  50 /*
  51   Starts = -----------------------------------M----------------------------
  52   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  53   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  54   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
  55
  56 4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the
  57 Mycoplasma/Spiroplasma Code (transl_table=4)
  58 */
  59 static
  60 char *AA4 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
  61 /*
  62   Starts = --MM---------------M------------MMMM---------------M------------
  63   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  64   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  65   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
  66
  67 5. The Invertebrate Mitochondrial Code (transl_table=5)
  68 */
  69 static
  70 char *AA5 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG";
  71 /*
  72   Starts = ---M----------------------------MMMM---------------M------------
  73   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  74   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  75   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
  76
  77 6. The Ciliate, Dasycladacean and Hexamita Nuclear Code (transl_table=6)
  78 */
  79 static
  80 char *AA6 ="FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
  81 /*
  82   Starts = -----------------------------------M----------------------------
  83   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  84   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  85   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
  86
  87 9. The Echinoderm Mitochondrial Code (transl_table=9)
  88 */
  89 static
  90 char *AA7 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG";
  91 /*
  92   Starts = -----------------------------------M----------------------------
  93   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  94   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  95   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
  96
  97 10. The Euplotid Nuclear Code (transl_table=10)
  98 */
  99 static
 100 char *AA10="FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
 101 /*
 102   Starts = -----------------------------------M----------------------------
 103   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 104   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 105   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 106
 107 11. The Bacterial "Code" (transl_table=11)
 108 */
 109 static
 110 char *AA11="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
 111 /*
 112   Starts = ---M---------------M------------MMMM---------------M------------
 113   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 114   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 115   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 116
 117 12. The Alternative Yeast Nuclear Code (transl_table=12)
 118 */
 119 static
 120 char *AA12 ="FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
 121 /*
 122   Starts = -------------------M---------------M----------------------------
 123   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 124   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 125   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 126
 127 13. The Ascidian Mitochondrial Code (transl_table=13)
 128 */
 129 static
 130 char *AA13="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG";
 131 /*
 132   Starts = -----------------------------------M----------------------------
 133   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 134   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 135   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 136
 137 14. The Flatworm Mitochondrial Code (transl_table=14)
 138 */
 139 static
 140 char *AA14 ="FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG";
 141 /*
 142   Starts = -----------------------------------M----------------------------
 143   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 144   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 145   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 146
 147 15. Blepharisma Nuclear Code (transl_table=15)
 148 */
 149 static
 150 char *AA15="FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
 151 /*
 152   Starts = -----------------------------------M----------------------------
 153   Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 154   Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 155   Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 156 */
 157
 158 static
 159 char *AA16 ="FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
 160 /*
 161   id 16 ,
 162   name "Chlorophycean Mitochondrial" ,
 163   sncbieaa "-----------------------------------M----------------------------"
 164   -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 165   -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 166   -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 167 */
 168
 169 static
 170 char *AA21 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG";
 171 /*
 172   name "Trematode Mitochondrial" ,
 173   id 21 ,
 174   sncbieaa "-----------------------------------M---------------M------------"
 175   -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 176   -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 177   -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 178 */
 179
 180 static
 181 char *AA22 ="FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
 182 /*
 183   name "Scenedesmus obliquus Mitochondrial" ,
 184   id 22 ,
 185   sncbieaa "-----------------------------------M----------------------------"
 186   -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 187   -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 188   -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 189 */
 190
 191 static
 192 char *AA23 ="FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
 193 /*
 194   name "Thraustochytrium Mitochondrial" ,
 195   id 23 ,
 196   sncbieaa "--------------------------------M--M---------------M------------"
 197   -- Base1  TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 198   -- Base2  TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 199   -- Base3  TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 200 */
 201
 202
 203 static char aacmap[64]={
 204   'K','N','K','N','T','T','T','T','R','S','R','S','I','I','M','I',
 205   'Q','H','Q','H','P','P','P','P','R','R','R','R','L','L','L','L',
 206   'E','D','E','D','A','A','A','A','G','G','G','G','V','V','V','V',
 207   '*','Y','*','Y','S','S','S','S','*','C','W','C','L','F','L','F'
 208 };
 209
 210 static int aamap[64];   /* integer aa values */
 211 static int aamapr[64]; /* reverse sequence map */
 212
 213 /* tnt is used only by aatran.c. It must be consistent with lascii and
 214 the nt alphabet. It uses 3,3 because T and U are considered separately
 215 */
 216 static int tnt[]={0,0,1,2,3,3,0,1,0,0,1,2,0,0,0,1,0,0,
 217                     0,1,2,3,3,0,1,0,0,1,2,0,0,0,1,0,0};
 218
 219 static int debug_set;
 220
 221 int
 222 aatran(const unsigned char *ntseq, unsigned char *aaseq, int maxs, int frame)
 223 {
 224   int iaa, im, nna, i;
 225   register int *nnp;
 226   const unsigned char *nts0;
 227   register int *aamp;
 228   register unsigned char *aap;
 229
 230   iaa=nna=(maxs-(frame<3?frame:frame-3))/3;
 231   if (nna <= 3 ) {
 232     aaseq[0]=EOSEQ;
 233     return 0;
 234   }
 235
 236   nnp = tnt;
 237
 238   if (frame < 3) {
 239     aamp = aamap;
 240     nts0 = &ntseq[frame];
 241     aap = aaseq;
 242     while (nna--) {
 243       im = nnp[*nts0++]<<4;
 244       im += nnp[*nts0++]<<2;
 245       im += nnp[*nts0++];
 246       *aap++ = aamp[im];
 247
 248       /* this check is included because of a bug in tfasty
 249          which occurs only during the alignment process */
 250
 251 #ifdef DEBUG
 252       if (debug_set && aamp[im] > MAXUC) {
 253         fprintf(stderr,"faatran: %d %d %d %d %d?%d\n",
 254                 *(nts0-3),*(nts0-2),*(nts0-1), im, aamp[im],aamap[im]);
 255
 256         /* this allows recovery, but should not be done frequently */
 257         for (i=0; i<64; i++) {
 258           aamap[i]=aascii[aacmap[i]];
 259           aamapr[i]=aascii[aacmap[(~i)&63]];
 260         }
 261         *(aap-1) = aamp[im];
 262       }
 263 #endif
 264     }
 265   }
 266   else {
 267     aamp = aamapr;
 268     nts0 = &ntseq[maxs-(frame-3)];
 269     aap = aaseq;
 270     while (nna--) {
 271       im = nnp[*--nts0]<<4;
 272       im += nnp[*--nts0]<<2;
 273       im += nnp[*--nts0];
 274       *aap++ = aamp[im];
 275       /* this check is included because of a bug in tfasty
 276          which occurs only during the alignment process */
 277
 278 #ifdef DEBUG
 279       if (debug_set && aamp[im] > MAXUC) {
 280         fprintf(stderr,"faatran: %d %d %d %d %d?%d\n",
 281                 *(nts0-3),*(nts0-2),*(nts0-1), im, aamp[im],aamap[im]);
 282
 283         /* this allows recovery, but should not be done frequently */
 284         for (i=0; i<64; i++) {
 285           aamap[i]=aascii[aacmap[i]];
 286           aamapr[i]=aascii[aacmap[(~i)&63]];
 287         }
 288         *(aap-1) = aamp[im];
 289       }
 290 #endif
 291     }
 292   }
 293   aaseq[iaa]=EOSEQ;
 294   return iaa;
 295 }
 296
 297 /* slower version that masks out NNN,XXX */
 298
 299 /*                - A C G T U R Y M W S K D H V B N X */
 300 static int snt[]={0,0,1,2,3,3,0,1,0,0,4,4,4,4,4,4,4,4};
 301
 302 int
 303 saatran(const unsigned char *ntseq,
 304         unsigned char *aaseq, int maxs, int frame)
 305 {
 306   int iaa, im, it, nna, xflag;
 307   register int *nnp;
 308   const unsigned char *nts0;
 309   register int *aamp;
 310   register unsigned char *aap;
 311
 312   iaa=nna=(maxs-(frame<3?frame:frame-3))/3;
 313   if (nna <= 3 ) {
 314     aaseq[0]=EOSEQ;
 315     return 0;
 316   }
 317
 318   nnp = snt;
 319   if (frame < 3) {
 320     aamp = aamap;
 321     nts0 = &ntseq[frame];
 322     aap = aaseq;
 323     while (nna--) {
 324       xflag = 0;
 325       if ((it=nnp[*nts0++])<4) {im = it<<4;}
 326       else {xflag = 1; im=0;}
 327       if ((it=nnp[*nts0++])<4) {im += it<<2;}
 328       else xflag = 1;
 329       if ((it=nnp[*nts0++])<4) {im += it;}
 330       else xflag = 1;
 331       if (xflag) *aap++ = aascii['X'];
 332       else *aap++ = aamp[im];
 333     }
 334   }
 335   else {
 336     aamp = aamapr;
 337     nts0 = &ntseq[maxs-(frame-3)];
 338     aap = aaseq;
 339     while (nna--) {
 340       xflag = 0;
 341       if ((it=nnp[*--nts0]) < 4) im = it<<4;
 342       else {xflag = 1; im=0;}
 343       if ((it=nnp[*--nts0]) < 4) im += it<<2;
 344       else xflag = 1;
 345       if ((it=nnp[*--nts0]) < 4) im += it;
 346       else xflag = 1;
 347       if (xflag) *aap++ = aascii['X'];
 348       else *aap++ = aamp[im];
 349     }
 350   }
 351   aaseq[iaa]=EOSEQ;
 352   return iaa;
 353 }
 354
 355 void
 356 aainit(int tr_type, int debug)
 357 {
 358   int i,j;
 359   char *aasmap;
 360   int imap[4]={3,1,0,2}, i0, i1, i2, ii;
 361
 362   debug_set = debug;
 363
 364   aasmap = AA1;
 365   if (tr_type > 0) {
 366     /* need to put in a new translation table */
 367     switch (tr_type) {
 368     case 1: aasmap = AA1; break;
 369     case 2: aasmap = AA2; break;
 370     case 3: aasmap = AA3; break;
 371     case 4: aasmap = AA4; break;
 372     case 5: aasmap = AA5; break;
 373     case 6: aasmap = AA6; break;
 374     case 7: aasmap = AA7; break;
 375     case 10: aasmap = AA10; break;
 376     case 11: aasmap = AA11; break;
 377     case 12: aasmap = AA12; break;
 378     case 13: aasmap = AA13; break;
 379     case 14: aasmap = AA14; break;
 380     case 15: aasmap = AA15; break;
 381     case 16: aasmap = AA16; break;
 382     case 21: aasmap = AA21; break;
 383     case 22: aasmap = AA22; break;
 384     case 23: aasmap = AA23; break;
 385
 386     default: aasmap = AA1; break;
 387     }
 388
 389     if (debug) fprintf(stderr," codon table: %d\n     new old\n",tr_type);
 390     for (i0 = 0; i0 < 4; i0++)
 391       for (i1 = 0; i1 < 4; i1++)
 392         for (i2 = 0; i2 < 4; i2++) {
 393           ii = (imap[i0]<<4) + (imap[i1]<<2) + imap[i2];
 394           if (debug &&  aacmap[ii] != *aasmap)
 395             fprintf(stderr," %c%c%c: %c - %c\n",
 396                     nt[imap[i0]+1],nt[imap[i1]+1],nt[imap[i2]+1],
 397                     *aasmap,aacmap[ii]);
 398           aacmap[ii]= *aasmap++;
 399         }
 400
 401     /*
 402     for (i=0; i<64; i++) {
 403       fprintf(stderr,"'%c',",aacmap[i]);
 404       if ((i%16)==15) fputc('\n',stderr);
 405     }
 406     fputc('\n',stderr);
 407     */
 408   }
 409   for (i=0; i<64; i++) {
 410     aamap[i]=aascii[aacmap[i]];
 411     aamapr[i]=aascii[aacmap[(~i)&63]];
 412   }
 413 }
 414
 415 void
 416 aagetmap(char *to, int n)
 417 {
 418   int i;
 419   for (i=0; i<n; i++) to[i] = aacmap[i];
 420 }