binaries/src/mafft/core/setcore.c

   1 #include "mltaln.h"
   2
   3 #define DEBUG 0
   4 #define IODEBUG 0
   5 #define SCOREOUT 1
   6
   7 double corethr;
   8 int coreext;
   9
  10 void arguments( int argc, char *argv[] )
  11 {
  12     int c;
  13
  14         fftkeika = 1;
  15         constraint = 0;
  16         nblosum = 62;
  17         fmodel = 0;
  18         calledByXced = 0;
  19         devide = 0;
  20         use_fft = 0;
  21         fftscore = 1;
  22         fftRepeatStop = 0;
  23         fftNoAnchStop = 0;
  24     weight = 3;
  25     utree = 1;
  26         tbutree = 1;
  27     refine = 0;
  28     check = 1;
  29     cut = 0.0;
  30     disp = 0;
  31     outgap = 1;
  32     alg = 'A';
  33     mix = 0;
  34         tbitr = 0;
  35         scmtd = 5;
  36         tbweight = 0;
  37         tbrweight = 3;
  38         checkC = 0;
  39         treemethod = 'x';
  40         contin = 0;
  41         scoremtx = 0;
  42         kobetsubunkatsu = 0;
  43         dorp = NOTSPECIFIED;
  44         ppenalty = NOTSPECIFIED;
  45         ppenalty_ex = NOTSPECIFIED;
  46         poffset = NOTSPECIFIED;
  47         kimuraR = NOTSPECIFIED;
  48         pamN = NOTSPECIFIED;
  49         geta2 = GETA2;
  50         fftWinSize = NOTSPECIFIED;
  51         fftThreshold = NOTSPECIFIED;
  52         corethr = .5;
  53         coreext = 0;
  54
  55     while( --argc > 0 && (*++argv)[0] == '-' )
  56         {
  57         while ( ( c = *++argv[0] ) )
  58                 {
  59             switch( c )
  60             {
  61                                 case 'f':
  62                                         ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
  63                                         fprintf( stderr, "ppenalty = %d\n", ppenalty );
  64                                         --argc;
  65                                         goto nextoption;
  66                                 case 'g':
  67                                         ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
  68                                         fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
  69                                         --argc;
  70                                         goto nextoption;
  71                                 case 'h':
  72                                         poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
  73                                         fprintf( stderr, "poffset = %d\n", poffset );
  74                                         --argc;
  75                                         goto nextoption;
  76                                 case 'k':
  77                                         kimuraR = atoi( *++argv );
  78                                         fprintf( stderr, "kimuraR = %d\n", kimuraR );
  79                                         --argc;
  80                                         goto nextoption;
  81                                 case 'b':
  82                                         nblosum = atoi( *++argv );
  83                                         scoremtx = 1;
  84                                         fprintf( stderr, "blosum %d\n", nblosum );
  85                                         --argc;
  86                                         goto nextoption;
  87                                 case 'j':
  88                                         pamN = atoi( *++argv );
  89                                         scoremtx = 0;
  90                                         fprintf( stderr, "jtt %d\n", pamN );
  91                                         --argc;
  92                                         goto nextoption;
  93                                 case 'l':
  94                                         fastathreshold = atof( *++argv );
  95                                         constraint = 2;
  96                                         fprintf( stderr, "weighti = %f\n", fastathreshold );
  97                                         --argc;
  98                                         goto nextoption;
  99                                 case 'i':
 100                                         corethr = atof( *++argv );
 101                                         fprintf( stderr, "corethr = %f\n", corethr );
 102                                         --argc;
 103                                         goto nextoption;
 104                                 case 'm':
 105                                         fmodel = 1;
 106                                         break;
 107                                 case 'c':
 108                                         coreext = 1;
 109                                         break;
 110                                 case 'r':
 111                                         fmodel = -1;
 112                                         break;
 113                                 case 'D':
 114                                         dorp = 'd';
 115                                         break;
 116                                 case 'P':
 117                                         dorp = 'p';
 118                                         break;
 119                                 case 'e':
 120                                         fftscore = 0;
 121                                         break;
 122                                 case 'O':
 123                                         fftNoAnchStop = 1;
 124                                         break;
 125                                 case 'R':
 126                                         fftRepeatStop = 1;
 127                                         break;
 128                                 case 'Q':
 129                                         calledByXced = 1;
 130                                         break;
 131                                 case 's':
 132                                         treemethod = 's';
 133                                         break;
 134                                 case 'x':
 135                                         treemethod = 'x';
 136                                         break;
 137                                 case 'p':
 138                                         treemethod = 'p';
 139                                         break;
 140                                 case 'a':
 141                                         alg = 'a';
 142                                         break;
 143                                 case 'A':
 144                                         alg = 'A';
 145                                         break;
 146                                 case 'S':
 147                                         alg = 'S';
 148                                         break;
 149                                 case 'C':
 150                                         alg = 'C';
 151                                         break;
 152                                 case 'F':
 153                                         use_fft = 1;
 154                                         break;
 155                                 case 'v':
 156                                         tbrweight = 3;
 157                                         break;
 158                                 case 'd':
 159                                         disp = 1;
 160                                         break;
 161                                 case 'o':
 162                                         outgap = 0;
 163                                         break;
 164 /* Modified 01/08/27, default: user tree */
 165                                 case 'J':
 166                                         tbutree = 0;
 167                                         break;
 168 /* modification end. */
 169                                 case 'z':
 170                                         fftThreshold = atoi( *++argv );
 171                                         --argc;
 172                                         goto nextoption;
 173                                 case 'w':
 174                                         fftWinSize = atoi( *++argv );
 175                                         --argc;
 176                                         goto nextoption;
 177                                 case 'Z':
 178                                         checkC = 1;
 179                                         break;
 180                 default:
 181                     fprintf( stderr, "illegal option %c\n", c );
 182                     argc = 0;
 183                     break;
 184             }
 185                 }
 186                 nextoption:
 187                         ;
 188         }
 189     if( argc == 1 )
 190     {
 191         cut = atof( (*argv) );
 192         argc--;
 193     }
 194     if( argc != 0 )
 195     {
 196         fprintf( stderr, "options: Check source file !\n" );
 197         exit( 1 );
 198     }
 199         if( tbitr == 1 && outgap == 0 )
 200         {
 201                 fprintf( stderr, "conflicting options : o, m or u\n" );
 202                 exit( 1 );
 203         }
 204         if( alg == 'C' && outgap == 0 )
 205         {
 206                 fprintf( stderr, "conflicting options : C, o\n" );
 207                 exit( 1 );
 208         }
 209 }
 210
 211
 212
 213 static void WriteOptions( FILE *fp )
 214 {
 215
 216         if( dorp == 'd' ) fprintf( fp, "DNA\n" );
 217         else
 218         {
 219                 if     ( scoremtx ==  0 ) fprintf( fp, "JTT %dPAM\n", pamN );
 220                 else if( scoremtx ==  1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
 221                 else if( scoremtx ==  2 ) fprintf( fp, "M-Y\n" );
 222         }
 223     fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
 224     if( use_fft ) fprintf( fp, "FFT on\n" );
 225
 226         fprintf( fp, "tree-base method\n" );
 227         if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
 228         else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
 229         if( tbitr || tbweight )
 230         {
 231                 fprintf( fp, "iterate at each step\n" );
 232                 if( tbitr && tbrweight == 0 ) fprintf( fp, "  unweighted\n" );
 233                 if( tbitr && tbrweight == 3 ) fprintf( fp, "  reversely weighted\n" );
 234                 if( tbweight ) fprintf( fp, "  weighted\n" );
 235                 fprintf( fp, "\n" );
 236         }
 237
 238          fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
 239
 240         if( alg == 'a' )
 241                 fprintf( fp, "Algorithm A\n" );
 242         else if( alg == 'A' )
 243                 fprintf( fp, "Algorithm A+\n" );
 244         else if( alg == 'S' )
 245                 fprintf( fp, "Apgorithm S\n" );
 246         else if( alg == 'C' )
 247                 fprintf( fp, "Apgorithm A+/C\n" );
 248         else
 249                 fprintf( fp, "Unknown algorithm\n" );
 250
 251         if( treemethod == 'x' )
 252                 fprintf( fp, "Tree = UPGMA (3).\n" );
 253         else if( treemethod == 's' )
 254                 fprintf( fp, "Tree = UPGMA (2).\n" );
 255         else if( treemethod == 'p' )
 256                 fprintf( fp, "Tree = UPGMA (1).\n" );
 257         else
 258                 fprintf( fp, "Unknown tree.\n" );
 259
 260     if( use_fft )
 261     {
 262         fprintf( fp, "FFT on\n" );
 263         if( dorp == 'd' )
 264             fprintf( fp, "Basis : 4 nucleotides\n" );
 265         else
 266         {
 267             if( fftscore )
 268                 fprintf( fp, "Basis : Polarity and Volume\n" );
 269             else
 270                 fprintf( fp, "Basis : 20 amino acids\n" );
 271         }
 272         fprintf( fp, "Threshold   of anchors = %d%%\n", fftThreshold );
 273         fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
 274     }
 275         else
 276         fprintf( fp, "FFT off\n" );
 277         fflush( fp );
 278 }
 279
 280
 281 int main( int argc, char *argv[] )
 282 {
 283         static int  nlen[M];
 284         static char **name, **seq;
 285         static char **oseq;
 286         static double **pscore;
 287         static double *eff;
 288         static double **node0, **node1;
 289         static double *gapc;
 290         static double *avgap;
 291         double tmpavgap;
 292         int i, j, m, goffset;
 293         static int ***topol;
 294         static double **len;
 295         FILE *prep;
 296         char c;
 297         int corestart, coreend;
 298         int alloclen;
 299         int winsize;
 300         char *pt, *ot;
 301         double gapmin;
 302
 303         arguments( argc, argv );
 304
 305         getnumlen( stdin );
 306         rewind( stdin );
 307
 308         if( njob < 2 )
 309         {
 310                 fprintf( stderr, "At least 2 sequences should be input!\n"
 311                                                  "Only %d sequence found.\n", njob );
 312                 exit( 1 );
 313         }
 314
 315         seq = AllocateCharMtx( njob, nlenmax*9+1 );
 316         name = AllocateCharMtx( njob, B+1 );
 317         oseq = AllocateCharMtx( njob, nlenmax*9+1 );
 318         alloclen = nlenmax*9;
 319
 320         topol = AllocateIntCub( njob, 2, njob );
 321         len = AllocateDoubleMtx( njob, 2 );
 322         pscore = AllocateDoubleMtx( njob, njob );
 323         eff = AllocateDoubleVec( njob );
 324         node0 = AllocateDoubleMtx( njob, njob );
 325         node1 = AllocateDoubleMtx( njob, njob );
 326         gapc = AllocateDoubleVec( alloclen );
 327         avgap = AllocateDoubleVec( alloclen );
 328
 329 #if 0
 330         Read( name, nlen, seq );
 331 #else
 332         readData_pointer( stdin, name, nlen, seq );
 333 #endif
 334
 335         constants( njob, seq );
 336
 337 #if 0
 338         fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
 339 #endif
 340
 341         initSignalSM();
 342
 343         initFiles();
 344
 345         WriteOptions( trap_g );
 346
 347         c = seqcheck( seq );
 348         if( c )
 349         {
 350                 fprintf( stderr, "Illeagal character %c\n", c );
 351                 exit( 1 );
 352         }
 353
 354         writePre( njob, name, nlen, seq, 0 );
 355
 356         if( tbutree == 0 )
 357         {
 358                 for( i=1; i<njob; i++ )
 359                 {
 360                         if( nlen[i] != nlen[0] )
 361                         {
 362                                 fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
 363                                 exit( 1 );
 364                         }
 365                 }
 366                 for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
 367                 {
 368                 /*
 369                         pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
 370                 */
 371                         pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
 372                 }
 373         }
 374         else
 375         {
 376                 fprintf( stderr, "Loading 'hat2' ... " );
 377                 prep = fopen( "hat2", "r" );
 378                 if( prep == NULL ) ErrorExit( "Make hat2." );
 379                 readhat2_pointer( prep, njob, name, pscore );
 380                 fclose( prep );
 381                 fprintf( stderr, "done.\n" );
 382
 383 #if 0
 384                 prep = fopen( "hat2_check", "w" );
 385                 WriteHat2( prep, njob, name, pscore );
 386                 fclose( prep );
 387 #endif
 388
 389         }
 390
 391         fprintf( stderr, "Constructing dendrogram ... " );
 392         if( treemethod == 'x' )
 393                 supg( njob, pscore, topol, len );
 394         else if( treemethod == 's' )
 395                 spg( njob, pscore, topol, len );
 396         else if( treemethod == 'p' )
 397                 upg2( njob, pscore, topol, len );
 398         else
 399                 ErrorExit( "Incorrect tree\n" );
 400         fprintf( stderr, "done.\n" );
 401
 402         countnode( njob, topol, node0 );
 403         if( tbrweight )
 404         {
 405                 weight = 3;
 406 #if 0
 407                 utree = 0; counteff( njob, topol, len, eff ); utree = 1;
 408 #else
 409                 counteff_simple( njob, topol, len, eff );
 410 #endif
 411         }
 412         else
 413         {
 414                 for( i=0; i<njob; i++ ) eff[i] = 1.0;
 415         }
 416
 417
 418         for( i=0; i<nlenmax; i++ )
 419         {
 420                 gapc[i] = 0.0;
 421                 for( j=0; j<njob; j++ )
 422                 {
 423                         if( seq[j][i] == '-' ) gapc[i] += eff[j];
 424                 }
 425         }
 426
 427         gapmin = 1.0;
 428         winsize = fftWinSize;
 429         goffset = winsize/2;
 430         tmpavgap = 0.0;
 431         corestart = coreend = -1;
 432         for( i=0; i<winsize; i++ )
 433         {
 434                 tmpavgap += gapc[i];
 435         }
 436         for( i=winsize; i<nlenmax; i++ )
 437         {
 438                 m = i - goffset;
 439                 avgap[m] = tmpavgap / winsize;
 440 //              fprintf( stdout, "%d %f %f\n", m, avgap[m], gapc[i] );
 441                 if( avgap[m] < corethr )
 442                 {
 443                         if( corestart == -1 )
 444                                 corestart = i - winsize;
 445 //                      fprintf( stdout, "ok, gapmin = %f, corestart = %d, coreend = %d\n", gapmin, corestart, coreend );
 446                         if( avgap[m] < gapmin )
 447                         {
 448                                 gapmin = avgap[m];
 449                         }
 450                         coreend = i;
 451                 }
 452                 tmpavgap -= gapc[i-winsize];
 453                 tmpavgap += gapc[i];
 454         }
 455         if( corestart == -1 || coreend == -1 )
 456         {
 457                 corestart = 0;
 458                 coreend = nlenmax-1;
 459         }
 460
 461         for( i=0; i<njob; i++ )
 462         {
 463                 pt = oseq[i];
 464                 m = winsize;
 465                 while( m-- ) *pt++ = '-';
 466                 for( j=corestart; j<=coreend; j++ )
 467                         *pt++ = seq[i][j];
 468                 m = winsize;
 469                 while( m-- ) *pt++ = '-';
 470                 *pt = 0;
 471
 472                 ot = oseq[i]+winsize-1;
 473                 pt = seq[i]+corestart-1;
 474                 if( coreext ) m = winsize;
 475                 else m = 0;
 476                 while( m && --pt > seq[i] )
 477                         if( *pt != '-' )
 478                         {
 479                                 *ot-- = *pt;
 480                                 m--;
 481                         }
 482
 483                 ot = oseq[i]+winsize+coreend-corestart+1;
 484                 pt = seq[i]+coreend;
 485                 if( coreext ) m = winsize;
 486                 else m = 0;
 487                 while( m && *(++pt) )
 488                 {
 489                         if( *pt != '-' )
 490                         {
 491                                 *ot++ = *pt;
 492                                 m--;
 493                         }
 494                 }
 495                 fprintf( stdout, ">%s\n", name[i] );
 496                 fprintf( stdout, "%s\n", oseq[i] );
 497         }
 498
 499         exit( 1 );
 500
 501         SHOWVERSION;
 502         return( 0 );
 503 }