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pair2hat3s.c

#include "mltaln.h"

#define DEBUG 0
#define IODEBUG 0
#define SCOREOUT 1
#define TSUYOSAFACTOR 100


static char *pairfile;
static int nhomologs;

void strip( char *s )
{
      char *pt = s;
      while( *++pt )
            if( *pt == '\n' ) *pt = 0;
}

int searchused( char *q, char **keys, int n )
{
      int i;
      for( i=0; i<n; i++ )
      {
//          fprintf( stderr, "%s ? %s\n", q, names[i] );
            if( !strcmp( q, keys[i] ) ) return( i );
      }
      return( -1 );
}

void arguments( int argc, char *argv[] )
{
    int c;

      nhomologs = 2;
      inputfile = NULL;
      pairfile = NULL;
      fftkeika = 0;
      pslocal = -1000.0;
      constraint = 0;
      nblosum = 62;
      fmodel = 0;
      calledByXced = 0;
      devide = 0;
      use_fft = 0;
      fftscore = 1;
      fftRepeatStop = 0;
      fftNoAnchStop = 0;
    weight = 3;
    utree = 1;
      tbutree = 1;
    refine = 0;
    check = 1;
    cut = 0.0;
    disp = 0;
    outgap = 1;
    alg = 'A';
    mix = 0;
      tbitr = 0;
      scmtd = 5;
      tbweight = 0;
      tbrweight = 3;
      checkC = 0;
      treemethod = 'x';
      contin = 0;
      scoremtx = 1;
      kobetsubunkatsu = 0;
      divpairscore = 0;
      dorp = NOTSPECIFIED;
      ppenalty = NOTSPECIFIED;
      ppenalty_OP = NOTSPECIFIED;
      ppenalty_ex = NOTSPECIFIED;
      ppenalty_EX = NOTSPECIFIED;
      poffset = NOTSPECIFIED;
      kimuraR = NOTSPECIFIED;
      pamN = NOTSPECIFIED;
      geta2 = GETA2;
      fftWinSize = NOTSPECIFIED;
      fftThreshold = NOTSPECIFIED;

    while( --argc > 0 && (*++argv)[0] == '-' )
      {
        while ( c = *++argv[0] )
            {
            switch( c )
            {
                        case 'i':
                              inputfile = *++argv;
                              fprintf( stderr, "inputfile = %s\n", inputfile );
                              --argc;
                              goto nextoption;
                        case 'p':
                              pairfile = *++argv;
                              fprintf( stderr, "pairfile = %s\n", pairfile );
                              --argc;
                              goto nextoption;
                        case 't':
                              nhomologs = atoi( *++argv );
                              fprintf( stderr, "nhomologs = %f\n", nhomologs );
                              --argc;
                              goto nextoption;
                        case 'D':
                              dorp = 'd';
                              break;
                        case 'P':
                              dorp = 'p';
                              break;
                default:
                    fprintf( stderr, "illegal option %c\n", c );
                    argc = 0;
                    break;
            }
            }
            nextoption:
                  ;
      }
    if( argc == 1 )
    {
        cut = atof( (*argv) );
        argc--;
    }
    if( argc != 0 ) 
    {
        fprintf( stderr, "options: Check source file !\n" );
        exit( 1 );
    }
      if( tbitr == 1 && outgap == 0 )
      {
            fprintf( stderr, "conflicting options : o, m or u\n" );
            exit( 1 );
      }
      if( alg == 'C' && outgap == 0 )
      {
            fprintf( stderr, "conflicting options : C, o\n" );
            exit( 1 );
      }
}

int countamino( char *s, int end )
{
      int val = 0;
      while( end-- )
            if( *s++ != '-' ) val++;
      return( val );
}

static void pairalign( char name[M][B], int nlen[M], char **seq, double *effarr, int alloclen )
{
      FILE *tmpfp;
      char fn[100];
      static char dumm1[B], dumm0[B];
      int i, j, l, ilim;
      int clus1, clus2;
      char *res;
      int s1, s2, r1, r2, off1, off2;
      float pscore;
      FILE *trap;
      FILE *hat2p, *hat3p;
      static char name1[M][B], name2[M][B];
      static double *effarr1 = NULL;
      static double *effarr2 = NULL;
      char *aseq;
      float dumfl = 0.0;
      double total;
      char *pt, *pt2;
      static char **pseq;
      char *hat2file = "hat2";
      LocalHom **localhomtable, *tmpptr;
      char **usedseqs;
      char **usednames;
      int nused;
      double tsuyosa;

      tsuyosa = (double)nhomologs * (nhomologs-1) / njob * TSUYOSAFACTOR;
      fprintf( stderr, "tsuyosa = %f\n", tsuyosa );
      localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
      for( i=0; i<njob; i++)
      {
            localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
            for( j=0; j<njob; j++)
            {
                  localhomtable[i][j].start1 = -1;
                  localhomtable[i][j].end1 = -1;
                  localhomtable[i][j].start2 = -1; 
                  localhomtable[i][j].end2 = -1; 
                  localhomtable[i][j].opt = -1.0;
                  localhomtable[i][j].next = NULL;
            }
      }

      if( effarr1 == NULL ) 
      {
            effarr1 = AllocateDoubleVec( njob );
            effarr2 = AllocateDoubleVec( njob );
            pseq = AllocateCharMtx( 2, nlenmax*9+1 );
            aseq = AllocateCharVec( nlenmax*9+1 );
            usedseqs = AllocateCharMtx( njob, nlenmax*9+1 );
            usednames = AllocateCharMtx( njob, B );
#if 0
#else
#endif
      }

#if 0
      fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
#endif

#if 0
      for( i=0; i<njob; i++ )
            fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
#endif


//    writePre( njob, name, nlen, aseq, 0 );

      fprintf( stderr, "opening %s\n", pairfile  );
      tmpfp = fopen( pairfile, "r" );
      if( !tmpfp )
      {
            fprintf( stderr, "Cannot open %s\n", pairfile );
            exit( 1 );
      }
      searchKUorWA( tmpfp );
      hat3p = fopen( "hat3", "w" );
      if( !hat3p ) ErrorExit( "Cannot open hat3." );
      nused = 0;
      while( 1 )
      {
            res = fgets( dumm0, B-1, tmpfp );
            strip( dumm0 );
            if( res == NULL )
            {
                  break;
            }
            load1SeqWithoutName_new( tmpfp, pseq[0] );
            gappick0( aseq, pseq[0] );
            i =  searchused( aseq, usedseqs, nused );
            if( i == -1 )
            {
                  strcpy( usednames[nused], dumm0+1 );
                  strcpy( usedseqs[nused], aseq );
                  i = nused;
                  nused++;
            }
            fprintf( stderr, "i = %d\n", i );

            res = fgets( dumm1, B-1, tmpfp );
            strip( dumm1 );
            if( res == NULL )
            {
                  fprintf( stderr, "ERROR: The number of sequences in %s must be even.\n", pairfile );
                  exit( 1 );
            }
            load1SeqWithoutName_new( tmpfp, pseq[1] );
            gappick0( aseq, pseq[1] );
            j =  searchused( aseq, usedseqs, nused );
            if( j == -1 )
            {
                  strcpy( usednames[nused], dumm1+1 );
                  strcpy( usedseqs[nused], aseq );
                  j = nused;
                  nused++;
            }
            fprintf( stderr, "j = %d\n", j );

            if( strlen( pseq[0] ) != strlen( pseq[1] ) )
            {
                  fprintf( stderr, "Not aligned,  %s - %s\n", dumm0, dumm1 );
                  exit( 1 );
            }


            fprintf( stderr, "adding %d-%d\n", i, j );
            putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
            for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
            {
                  if( tmpptr->opt == -1.0 ) continue;
                  fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next ); 
            }
      }
      fclose( tmpfp );
      fclose( hat3p );

      for( i=0; i<nused; i++ )
            fprintf( stdout, ">%s\n%s\n", usednames[i], usedseqs[i] );


#if 0
      fprintf( stderr, "##### writing hat3\n" );
      hat3p = fopen( "hat3", "w" );
      if( !hat3p ) ErrorExit( "Cannot open hat3." );
      ilim = njob-1;    
      for( i=0; i<ilim; i++ ) 
      {
            for( j=i+1; j<njob; j++ )
            {
                  for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
                  {
                        if( tmpptr->opt == -1.0 ) continue;
                        fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, tmpptr->next ); 
                  }
            }
      }
      fclose( hat3p );
#endif
#if DEBUG
      fprintf( stderr, "calling FreeLocalHomTable\n" );
#endif
      FreeLocalHomTable( localhomtable, njob );
#if DEBUG
      fprintf( stderr, "done. FreeLocalHomTable\n" );
#endif
}

static void WriteOptions( FILE *fp )
{

      if( dorp == 'd' ) fprintf( fp, "DNA\n" );
      else
      {
            if     ( scoremtx ==  0 ) fprintf( fp, "JTT %dPAM\n", pamN );
            else if( scoremtx ==  1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
            else if( scoremtx ==  2 ) fprintf( fp, "M-Y\n" );
      }
    fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
    if( use_fft ) fprintf( fp, "FFT on\n" );

      fprintf( fp, "tree-base method\n" );
      if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
      else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
      if( tbitr || tbweight ) 
      {
            fprintf( fp, "iterate at each step\n" );
            if( tbitr && tbrweight == 0 ) fprintf( fp, "  unweighted\n" ); 
            if( tbitr && tbrweight == 3 ) fprintf( fp, "  reversely weighted\n" ); 
            if( tbweight ) fprintf( fp, "  weighted\n" ); 
            fprintf( fp, "\n" );
      }

       fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );

      if( alg == 'a' )
            fprintf( fp, "Algorithm A\n" );
      else if( alg == 'A' ) 
            fprintf( fp, "Algorithm A+\n" );
      else if( alg == 'S' ) 
            fprintf( fp, "Apgorithm S\n" );
      else if( alg == 'C' ) 
            fprintf( fp, "Apgorithm A+/C\n" );
      else
            fprintf( fp, "Unknown algorithm\n" );

      if( treemethod == 'x' )
            fprintf( fp, "Tree = UPGMA (3).\n" );
      else if( treemethod == 's' )
            fprintf( fp, "Tree = UPGMA (2).\n" );
      else if( treemethod == 'p' )
            fprintf( fp, "Tree = UPGMA (1).\n" );
      else
            fprintf( fp, "Unknown tree.\n" );

    if( use_fft )
    {
        fprintf( fp, "FFT on\n" );
        if( dorp == 'd' )
            fprintf( fp, "Basis : 4 nucleotides\n" );
        else
        {
            if( fftscore )
                fprintf( fp, "Basis : Polarity and Volume\n" );
            else
                fprintf( fp, "Basis : 20 amino acids\n" );
        }
        fprintf( fp, "Threshold   of anchors = %d%%\n", fftThreshold );
        fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
    }
      else
        fprintf( fp, "FFT off\n" );
      fflush( fp );
}
       

int main( int argc, char *argv[] )
{
      static int  nlen[M];    
      static char name[M][B], **seq;
      static char **bseq;
      static double **pscore;
      static double *eff;
      static double **node0, **node1;
      int i, j;
      int identity;
      static int ***topol;
      static double **len;
      char c;
      int alloclen;
      double total;
      FILE *prep, *infp;

      arguments( argc, argv );

      if( inputfile )
      {
            infp = fopen( inputfile, "r" );
            if( !infp )
            {
                  fprintf( stderr, "Cannot open %s\n", inputfile );
                  exit( 1 );
            }
      }
      else
            infp = stdin;

      if( !pairfile )
      {
            fprintf( stderr, "Usage: %s -p pairfile -i inputfile \n", argv[0] );
            exit( 1 );
      }

      getnumlen( infp );
      rewind( infp );

      if( njob < 2 )
      {
            fprintf( stderr, "At least 2 sequences should be input!\n"
                                     "Only %d sequence found.\n", njob ); 
            exit( 1 );
      }

      seq = AllocateCharMtx( njob, nlenmax*9+1 );
      bseq = AllocateCharMtx( njob, nlenmax*9+1 );
      alloclen = nlenmax*9;

      eff = AllocateDoubleVec( njob );

#if 0
      Read( name, nlen, seq );
#else
      readData( infp, name, nlen, seq );
#endif
      fclose( infp );

      constants( njob, seq );

#if 0
      fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
#endif

      initSignalSM();

      initFiles();

      WriteOptions( trap_g );

      c = seqcheck( seq );
      if( c )
      {
            fprintf( stderr, "Illeagal character %c\n", c );
            exit( 1 );
      }

//    writePre( njob, name, nlen, seq, 0 );

      for( i=0; i<njob; i++ ) eff[i] = 1.0;


      for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );


      pairalign( name, nlen, bseq, eff, alloclen );

      fprintf( trap_g, "done.\n" );
#if DEBUG
      fprintf( stderr, "closing trap_g\n" );
#endif
      fclose( trap_g );

#if IODEBUG
      fprintf( stderr, "OSHIMAI\n" );
#endif
      SHOWVERSION;
      return( 0 );
}

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