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527 lines
14 KiB
C
527 lines
14 KiB
C
#include "mltaln.h"
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#include "dp.h"
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#define MEMSAVE 1
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#define DEBUG 1
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#define USE_PENALTY_EX 1
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#define STOREWM 1
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#if 0
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static double singleribosumscore( int n1, int n2, char **s1, char **s2, double *eff1, double *eff2, int p1, int p2 )
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{
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double val;
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int i, j;
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int code1, code2;
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val = 0.0;
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for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
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{
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code1 = amino_n[(int)s1[i][p1]];
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if( code1 > 3 ) code1 = 36;
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code2 = amino_n[(int)s2[j][p2]];
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if( code2 > 3 ) code2 = 36;
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// fprintf( stderr, "'l'%c-%c: %f\n", s1[i][p1], s2[j][p2], (double)ribosumdis[code1][code2] );
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val += (double)ribosumdis[code1][code2] * eff1[i] * eff2[j];
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}
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return( val );
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}
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static double pairedribosumscore53( int n1, int n2, char **s1, char **s2, double *eff1, double *eff2, int p1, int p2, int c1, int c2 )
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{
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double val;
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int i, j;
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int code1o, code1u, code2o, code2u, code1, code2;
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val = 0.0;
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for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
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{
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code1o = amino_n[(int)s1[i][p1]];
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code1u = amino_n[(int)s1[i][c1]];
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if( code1o > 3 ) code1 = code1o = 36;
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else if( code1u > 3 ) code1 = 36;
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else code1 = 4 + code1o * 4 + code1u;
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code2o = amino_n[(int)s2[j][p2]];
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code2u = amino_n[(int)s2[j][c2]];
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if( code2o > 3 ) code2 = code1o = 36;
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else if( code2u > 3 ) code2 = 36;
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else code2 = 4 + code2o * 4 + code2u;
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// fprintf( stderr, "%c%c-%c%c: %f\n", s1[i][p1], s1[i][c1], s2[j][p2], s2[j][c2], (double)ribosumdis[code1][code2] );
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if( code1 == 36 || code2 == 36 )
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val += (double)n_dis[code1o][code2o] * eff1[i] * eff2[j];
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else
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val += (double)ribosumdis[code1][code2] * eff1[i] * eff2[j];
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}
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return( val );
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}
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static double pairedribosumscore35( int n1, int n2, char **s1, char **s2, double *eff1, double *eff2, int p1, int p2, int c1, int c2 )
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{
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double val;
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int i, j;
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int code1o, code1u, code2o, code2u, code1, code2;
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val = 0.0;
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for( i=0; i<n1; i++ ) for( j=0; j<n2; j++ )
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{
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code1o = amino_n[(int)s1[i][p1]];
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code1u = amino_n[(int)s1[i][c1]];
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if( code1o > 3 ) code1 = code1o = 36;
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else if( code1u > 3 ) code1 = 36;
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else code1 = 4 + code1u * 4 + code1o;
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code2o = amino_n[(int)s2[j][p2]];
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code2u = amino_n[(int)s2[j][c2]];
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if( code2o > 3 ) code2 = code1o = 36;
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else if( code2u > 3 ) code2 = 36;
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else code2 = 4 + code2u * 4 + code2o;
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// fprintf( stderr, "%c%c-%c%c: %f\n", s1[i][p1], s1[i][c1], s2[j][p2], s2[j][c2], (double)ribosumdis[code1][code2] );
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if( code1 == 36 || code2 == 36 )
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val += (double)n_dis[code1o][code2o] * eff1[i] * eff2[j];
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else
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val += (double)ribosumdis[code1][code2] * eff1[i] * eff2[j];
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}
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return( val );
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}
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#endif
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static void mccaskillextract( char **seq, char **nogap, int nseq, RNApair **pairprob, RNApair ***single, int **sgapmap, double *eff )
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{
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int lgth;
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int nogaplgth;
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int i, j;
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int left, right, adpos;
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double prob;
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static TLS int *pairnum;
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RNApair *pt, *pt2;
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lgth = strlen( seq[0] );
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pairnum = calloc( lgth, sizeof( int ) );
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for( i=0; i<lgth; i++ ) pairnum[i] = 0;
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for( i=0; i<nseq; i++ )
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{
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nogaplgth = strlen( nogap[i] );
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for( j=0; j<nogaplgth; j++ ) for( pt=single[i][j]; pt->bestpos!=-1; pt++ )
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{
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left = sgapmap[i][j];
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right = sgapmap[i][pt->bestpos];
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prob = pt->bestscore;
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for( pt2=pairprob[left]; pt2->bestpos!=-1; pt2++ )
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if( pt2->bestpos == right ) break;
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// fprintf( stderr, "i,j=%d,%d, left=%d, right=%d, pt=%d, pt2->bestpos = %d\n", i, j, left, right, pt-single[i][j], pt2->bestpos );
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if( pt2->bestpos == -1 )
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{
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pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
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adpos = pairnum[left];
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pairnum[left]++;
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pairprob[left][adpos].bestscore = 0.0;
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pairprob[left][adpos].bestpos = right;
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pairprob[left][adpos+1].bestscore = -1.0;
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pairprob[left][adpos+1].bestpos = -1;
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pt2 = pairprob[left]+adpos;
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}
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else
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adpos = pt2-pairprob[left];
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pt2->bestscore += prob * eff[i];
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if( pt2->bestpos != right )
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{
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fprintf( stderr, "okashii!\n" );
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exit( 1 );
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}
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// fprintf( stderr, "adding %d-%d, %f\n", left, right, prob );
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// fprintf( stderr, "pairprob[0][0].bestpos=%d\n", pairprob[0][0].bestpos );
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// fprintf( stderr, "pairprob[0][0].bestscore=%f\n", pairprob[0][0].bestscore );
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}
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}
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// fprintf( stderr, "before taikakuka\n" );
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for( i=0; i<lgth; i++ ) for( j=0; j<pairnum[i]; j++ )
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{
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if( pairprob[i][j].bestpos > -1 )
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{
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// pairprob[i][j].bestscore /= (double)nseq;
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// fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, pairprob[i][j].bestpos, pairprob[i][j].bestscore, seq[0][i], seq[0][pairprob[i][j].bestpos] );
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}
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}
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#if 0
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for( i=0; i<lgth; i++ ) for( j=0; j<pairnum[i]; j++ )
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{
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right=pairprob[i][j].bestpos;
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if( right < i ) continue;
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fprintf( stderr, "no%d-%d, adding %d -> %d\n", i, j, right, i );
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pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
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pairprob[right][pairnum[right]].bestscore = pairprob[i][j].bestscore;
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pairprob[right][pairnum[right]].bestpos = i;
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pairnum[right]++;
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pairprob[right][pairnum[right]].bestscore = -1.0;
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pairprob[right][pairnum[right]].bestpos = -1;
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}
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#endif
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free( pairnum );
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}
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void rnaalifoldcall( char **seq, int nseq, RNApair **pairprob )
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{
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int lgth;
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int i;
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static TLS int *order = NULL;
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static TLS char **name = NULL;
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char gett[1000];
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FILE *fp;
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int left, right, dumm;
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double prob;
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static TLS int pid;
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static TLS char fnamein[100];
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static TLS char cmd[1000];
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static TLS int *pairnum;
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lgth = strlen( seq[0] );
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if( order == NULL )
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{
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pid = (int)getpid();
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sprintf( fnamein, "/tmp/_rnaalifoldin.%d", pid );
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order = AllocateIntVec( njob );
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name = AllocateCharMtx( njob, 10 );
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for( i=0; i<njob; i++ )
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{
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order[i] = i;
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sprintf( name[i], "seq%d", i );
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}
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}
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pairnum = calloc( lgth, sizeof( int ) );
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for( i=0; i<lgth; i++ ) pairnum[i] = 0;
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fp = fopen( fnamein, "w" );
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if( !fp )
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{
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fprintf( stderr, "Cannot open /tmp/_rnaalifoldin\n" );
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exit( 1 );
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}
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clustalout_pointer( fp, nseq, lgth, seq, name, NULL, NULL, order, 15 );
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fclose( fp );
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sprintf( cmd, "RNAalifold -p %s", fnamein );
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system( cmd );
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fp = fopen( "alifold.out", "r" );
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if( !fp )
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{
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fprintf( stderr, "Cannot open /tmp/_rnaalifoldin\n" );
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exit( 1 );
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}
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#if 0
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for( i=0; i<lgth; i++ ) // atode kesu
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{
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pairprob[i] = (RNApair *)realloc( pairprob[i], (2) * sizeof( RNApair ) ); // atode kesu
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pairprob[i][1].bestscore = -1.0;
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pairprob[i][1].bestpos = -1;
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}
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#endif
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while( 1 )
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{
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fgets( gett, 999, fp );
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if( gett[0] == '(' ) break;
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if( gett[0] == '{' ) break;
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if( gett[0] == '.' ) break;
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if( gett[0] == ',' ) break;
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if( gett[0] != ' ' ) continue;
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sscanf( gett, "%d %d %d %lf", &left, &right, &dumm, &prob );
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left--;
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right--;
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#if 0
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if( prob > 50.0 && prob > pairprob[left][0].bestscore )
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{
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pairprob[left][0].bestscore = prob;
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pairprob[left][0].bestpos = right;
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#else
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if( prob > 0.0 )
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{
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pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
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pairprob[left][pairnum[left]].bestscore = prob / 100.0;
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pairprob[left][pairnum[left]].bestpos = right;
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pairnum[left]++;
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pairprob[left][pairnum[left]].bestscore = -1.0;
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pairprob[left][pairnum[left]].bestpos = -1;
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fprintf( stderr, "%d-%d, %f\n", left, right, prob );
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pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
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pairprob[right][pairnum[right]].bestscore = prob / 100.0;
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pairprob[right][pairnum[right]].bestpos = left;
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pairnum[right]++;
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pairprob[right][pairnum[right]].bestscore = -1.0;
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pairprob[right][pairnum[right]].bestpos = -1;
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fprintf( stderr, "%d-%d, %f\n", left, right, prob );
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#endif
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}
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}
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fclose( fp );
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sprintf( cmd, "rm -f %s", fnamein );
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system( cmd );
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for( i=0; i<lgth; i++ )
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{
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if( (right=pairprob[i][0].bestpos) > -1 )
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{
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pairprob[right][0].bestpos = i;
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pairprob[right][0].bestscore = pairprob[i][0].bestscore;
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}
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}
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#if 0
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for( i=0; i<lgth; i++ ) // atode kesu
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if( pairprob[i][0].bestscore > -1 ) pairprob[i][0].bestscore = 1.0; // atode kesu
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#endif
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// fprintf( stderr, "after taikakuka in rnaalifoldcall\n" );
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// for( i=0; i<lgth; i++ )
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// {
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// fprintf( stderr, "pair of %d = %d (%f) %c:%c\n", i, pairprob[i][0].bestpos, pairprob[i][0].bestscore, seq[0][i], seq[0][pairprob[i][0].bestpos] );
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// }
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free( pairnum );
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}
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static void utot( int n, int l, char **s )
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{
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int i, j;
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for( i=0; i<l; i++ )
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{
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for( j=0; j<n; j++ )
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{
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if ( s[j][i] == 'a' ) s[j][i] = 'a';
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else if( s[j][i] == 't' ) s[j][i] = 't';
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else if( s[j][i] == 'u' ) s[j][i] = 't';
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else if( s[j][i] == 'g' ) s[j][i] = 'g';
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else if( s[j][i] == 'c' ) s[j][i] = 'c';
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else if( s[j][i] == '-' ) s[j][i] = '-';
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else s[j][i] = 'n';
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}
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}
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}
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void foldrna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***grouprna1, RNApair ***grouprna2, double **impmtx, int *gapmap1, int *gapmap2, RNApair *additionalpair )
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{
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int i, j;
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// int ui, uj;
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// int uiup, ujup;
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int uido, ujdo;
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static TLS char **useq1, **useq2;
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static TLS char **oseq1, **oseq2, **oseq1r, **oseq2r, *odir1, *odir2;
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static TLS RNApair **pairprob1, **pairprob2;
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static TLS RNApair *pairpt1, *pairpt2;
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int lgth1 = strlen( seq1[0] );
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int lgth2 = strlen( seq2[0] );
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static TLS double **impmtx2;
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static TLS double **map;
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// double lenfac;
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double prob;
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int **sgapmap1, **sgapmap2;
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// char *nogapdum;
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double **tbppmtx;
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// fprintf( stderr, "nseq1=%d, lgth1=%d\n", nseq1, lgth1 );
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useq1 = AllocateCharMtx( nseq1, lgth1+10 );
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useq2 = AllocateCharMtx( nseq2, lgth2+10 );
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oseq1 = AllocateCharMtx( nseq1, lgth1+10 );
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oseq2 = AllocateCharMtx( nseq2, lgth2+10 );
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oseq1r = AllocateCharMtx( nseq1, lgth1+10 );
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oseq2r = AllocateCharMtx( nseq2, lgth2+10 );
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odir1 = AllocateCharVec( lgth1+10 );
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odir2 = AllocateCharVec( lgth2+10 );
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sgapmap1 = AllocateIntMtx( nseq1, lgth1+1 );
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sgapmap2 = AllocateIntMtx( nseq2, lgth2+1 );
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// nogapdum = AllocateCharVec( MAX( lgth1, lgth2 ) );
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pairprob1 = (RNApair **)calloc( lgth1, sizeof( RNApair *) );
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pairprob2 = (RNApair **)calloc( lgth2, sizeof( RNApair *) );
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map = AllocateFloatMtx( lgth1, lgth2 );
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impmtx2 = AllocateFloatMtx( lgth1, lgth2 );
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tbppmtx = AllocateFloatMtx( lgth1, lgth2 );
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for( i=0; i<nseq1; i++ ) strcpy( useq1[i], seq1[i] );
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for( i=0; i<nseq2; i++ ) strcpy( useq2[i], seq2[i] );
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for( i=0; i<nseq1; i++ ) strcpy( oseq1[i], seq1[i] );
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for( i=0; i<nseq2; i++ ) strcpy( oseq2[i], seq2[i] );
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for( i=0; i<nseq1; i++ ) commongappick_record( 1, useq1+i, sgapmap1[i] );
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for( i=0; i<nseq2; i++ ) commongappick_record( 1, useq2+i, sgapmap2[i] );
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for( i=0; i<lgth1; i++ )
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{
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pairprob1[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
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pairprob1[i][0].bestpos = -1;
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pairprob1[i][0].bestscore = -1;
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}
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for( i=0; i<lgth2; i++ )
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{
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pairprob2[i] = (RNApair *)calloc( 1, sizeof( RNApair ) );
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pairprob2[i][0].bestpos = -1;
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pairprob2[i][0].bestscore = -1;
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}
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utot( nseq1, lgth1, oseq1 );
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utot( nseq2, lgth2, oseq2 );
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// fprintf( stderr, "folding group1\n" );
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// rnalocal( oseq1, useq1, eff1, eff1, nseq1, nseq1, lgth1+10, pair1 );
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/* base-pairing probability of group 1 */
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if( rnaprediction == 'r' )
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rnaalifoldcall( oseq1, nseq1, pairprob1 );
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else
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mccaskillextract( oseq1, useq1, nseq1, pairprob1, grouprna1, sgapmap1, eff1 );
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// fprintf( stderr, "folding group2\n" );
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// rnalocal( oseq2, useq2, eff2, eff2, nseq2, nseq2, lgth2+10, pair2 );
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/* base-pairing probability of group 2 */
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if( rnaprediction == 'r' )
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rnaalifoldcall( oseq2, nseq2, pairprob2 );
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else
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mccaskillextract( oseq2, useq2, nseq2, pairprob2, grouprna2, sgapmap2, eff2 );
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#if 0
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makerseq( oseq1, oseq1r, odir1, pairprob1, nseq1, lgth1 );
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makerseq( oseq2, oseq2r, odir2, pairprob2, nseq2, lgth2 );
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fprintf( stderr, "%s\n", odir2 );
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for( i=0; i<nseq1; i++ )
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{
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fprintf( stdout, ">ori\n%s\n", oseq1[0] );
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fprintf( stdout, ">rev\n%s\n", oseq1r[0] );
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}
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|
#endif
|
|
|
|
/* similarity score */
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|
Lalignmm_hmout( oseq1, oseq2, eff1, eff2, nseq1, nseq2, 10000, NULL, NULL, NULL, NULL, map );
|
|
|
|
if( 1 )
|
|
{
|
|
if( RNAscoremtx == 'n' )
|
|
{
|
|
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
|
|
{
|
|
// impmtx2[i][j] = osoiaveragescore( nseq1, nseq2, oseq1, oseq2, eff1, eff2, i, j ) * consweight_multi;
|
|
impmtx2[i][j] = 0.0;
|
|
}
|
|
}
|
|
else if( RNAscoremtx == 'r' )
|
|
{
|
|
fprintf( stderr, "Unexpected error. Please contact katoh@ifrec.osaka-u.ac.jp\n" );
|
|
}
|
|
|
|
|
|
/* four-way consistency */
|
|
|
|
for( i=0; i<lgth1; i++ ) for( pairpt1=pairprob1[i]; pairpt1->bestpos!=-1; pairpt1++ )
|
|
{
|
|
|
|
// if( pairprob1[i] == NULL ) continue;
|
|
|
|
for( j=0; j<lgth2; j++ ) for( pairpt2=pairprob2[j]; pairpt2->bestpos!=-1; pairpt2++ )
|
|
{
|
|
// fprintf( stderr, "i=%d, j=%d, pn1=%d, pn2=%d\n", i, j, pairpt1-pairprob1[i], pairpt2-pairprob2[j] );
|
|
// if( pairprob2[j] == NULL ) continue;
|
|
|
|
uido = pairpt1->bestpos;
|
|
ujdo = pairpt2->bestpos;
|
|
prob = pairpt1->bestscore * pairpt2->bestscore;
|
|
// prob = 1.0;
|
|
// fprintf( stderr, "i=%d->uido=%d, j=%d->ujdo=%d\n", i, uido, j, ujdo );
|
|
|
|
// fprintf( stderr, "impmtx2[%d][%d] = %f\n", i, j, impmtx2[i][j] );
|
|
|
|
// if( i < uido && j > ujdo ) continue;
|
|
// if( i > uido && j < ujdo ) continue;
|
|
|
|
|
|
// posdistj = abs( ujdo-j );
|
|
|
|
// if( uido > -1 && ujdo > -1 )
|
|
if( uido > -1 && ujdo > -1 && ( ( i > uido && j > ujdo ) || ( i < uido && j < ujdo ) ) )
|
|
{
|
|
{
|
|
impmtx2[i][j] += MAX( 0, map[uido][ujdo] ) * consweight_rna * 600 * prob; // osoi
|
|
}
|
|
}
|
|
|
|
}
|
|
}
|
|
for( i=0; i<lgth1; i++ ) for( j=0; j<lgth2; j++ )
|
|
{
|
|
impmtx[i][j] += impmtx2[i][j];
|
|
// fprintf( stderr, "fastathreshold=%f, consweight_multi=%f, consweight_rna=%f\n", fastathreshold, consweight_multi, consweight_rna );
|
|
// impmtx[i][j] *= 0.5;
|
|
}
|
|
|
|
// impmtx[0][0] += 10000.0;
|
|
// impmtx[lgth1-1][lgth2-1] += 10000.0;
|
|
|
|
|
|
|
|
#if 0
|
|
fprintf( stdout, "#impmtx2 = \n" );
|
|
for( i=0; i<lgth1; i++ )
|
|
{
|
|
for( j=0; j<lgth2; j++ )
|
|
{
|
|
fprintf( stdout, "%d %d %f\n", i, j, impmtx2[i][j] );
|
|
}
|
|
fprintf( stdout, "\n" );
|
|
}
|
|
exit( 1 );
|
|
#endif
|
|
}
|
|
|
|
FreeCharMtx( useq1 );
|
|
FreeCharMtx( useq2 );
|
|
FreeCharMtx( oseq1 );
|
|
FreeCharMtx( oseq2 );
|
|
FreeCharMtx( oseq1r );
|
|
FreeCharMtx( oseq2r );
|
|
free( odir1 );
|
|
free( odir2 );
|
|
FreeFloatMtx( impmtx2 );
|
|
FreeFloatMtx( map );
|
|
FreeIntMtx( sgapmap1 );
|
|
FreeIntMtx( sgapmap2 );
|
|
FreeFloatMtx( tbppmtx );
|
|
|
|
for( i=0; i<lgth1; i++ ) free( pairprob1[i] );
|
|
for( i=0; i<lgth2; i++ ) free( pairprob2[i] );
|
|
free( pairprob1 );
|
|
free( pairprob2 );
|
|
}
|
|
|