static float callmxscarna( char **mseq1, char **mseq2, int alloclen ) { FILE *fp; int res; static char com[10000]; float value; t2u( *mseq1 ); t2u( *mseq2 ); fp = fopen( "_mxscarnain", "w" ); if( !fp ) { fprintf( stderr, "Cannot open _mxscarnain\n" ); exit( 1 ); } fprintf( fp, ">1\n" ); fprintf( fp, "%s\n", *mseq1 ); fprintf( fp, ">2\n" ); fprintf( fp, "%s\n", *mseq2 ); fclose( fp ); sprintf( com, "env PATH=%s mxscarna _mxscarnain > _mxscarnaout 2>/dev/null", whereispairalign ); res = system( com ); if( res ) { fprintf( stderr, "Error in mxscarna\n" ); exit( 1 ); } fp = fopen( "_mxscarnaout", "r" ); if( !fp ) { fprintf( stderr, "Cannot open _mxscarnaout\n" ); exit( 1 ); } fgets( com, 999, fp ); load1SeqWithoutName_new( fp, *mseq1 ); fgets( com, 999, fp ); load1SeqWithoutName_new( fp, *mseq2 ); fclose( fp ); // fprintf( stderr, "*mseq1 = %s\n", *mseq1 ); // fprintf( stderr, "*mseq2 = %s\n", *mseq2 ); value = (float)naivepairscore11( *mseq1, *mseq2, penalty ); return( value ); }
static void pairalign( char **name, int nlen[M], char **seq, double *effarr, int alloclen ) { FILE *tmpfp; static char dumm1[B], dumm0[B]; int i, j; char *res; FILE *hat3p; static double *effarr1 = NULL; static double *effarr2 = NULL; static char **pseq; LocalHom **localhomtable, *tmpptr; float pscore = 0.0; // by D.Mathog, aguess char *aseq = NULL; // by D.Mathog char **usedseqs = NULL; // by D.Mathog char **usednames = NULL; // by D.Mathog 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, (void *)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 }