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#include "mltaln.h"
#define DEBUG 0
static char *whereiscontrafold;
void unknown_n( char *out, char *in )
{
while( *in )
{
if( *in == 'a' || *in == 'A' )
*out = 'A';
else if( *in == 't' || *in == 'T' || *in == 'u' || *in == 'U' )
*out = 'U';
else if( *in == 'g' || *in == 'G' )
*out = 'G';
else if( *in == 'c' || *in == 'C' )
*out = 'C';
else if( *in == '-' )
*out = '-';
else
*out = 'N';
out++;
in++;
}
*out = 0;
}
void outcontrafold( FILE *fp, RNApair **pairprob, int length )
{
int i;
RNApair *pt;
for( i=0; i<length; i++ ) for( pt=pairprob[i]; pt->bestpos!=-1; pt++ )
{
if( pt->bestpos > i )
fprintf( fp, "%d %d %f\n", i, pt->bestpos, pt->bestscore );
}
}
#if 1
static void readcontrafold( FILE *fp, RNApair **pairprob, int length )
{
char gett[10000];
int *pairnum;
char *pt;
int i;
int left, right;
double prob;
pairnum = (int *)calloc( length, sizeof( int ) );
for( i=0; i<length; i++ ) pairnum[i] = 0;
while( 1 )
{
if( feof( fp ) ) break;
fgets( gett, 9999, fp );
// fprintf( stderr, "gett=%s\n", gett );
pt = gett;
sscanf( gett, "%d ", &left );
left--;
// fprintf( stderr, "left=%d\n", left );
pt = strchr( pt, ' ' ) + 1;
// fprintf( stderr, "pt=%s\n", pt );
while( (pt = strchr( pt, ' ' ) ) )
{
pt++;
// fprintf( stderr, "pt=%s\n", pt );
sscanf( pt, "%d:%lf", &right, &prob );
right--;
// fprintf( stderr, "%d-%d, %f\n", left, right, prob );
pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
pairprob[left][pairnum[left]].bestscore = prob;
pairprob[left][pairnum[left]].bestpos = right;
pairnum[left]++;
pairprob[left][pairnum[left]].bestscore = -1.0;
pairprob[left][pairnum[left]].bestpos = -1;
// fprintf( stderr, "%d-%d, %f\n", left, right, prob );
pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
pairprob[right][pairnum[right]].bestscore = prob;
pairprob[right][pairnum[right]].bestpos = left;
pairnum[right]++;
pairprob[right][pairnum[right]].bestscore = -1.0;
pairprob[right][pairnum[right]].bestpos = -1;
// fprintf( stderr, "%d-%d, %f\n", right, left, prob );
}
}
free( pairnum );
}
#endif
void arguments( int argc, char *argv[] )
{
int c;
inputfile = NULL;
dorp = NOTSPECIFIED;
kimuraR = NOTSPECIFIED;
pamN = NOTSPECIFIED;
whereiscontrafold = NULL;
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 'd':
whereiscontrafold = *++argv;
fprintf( stderr, "whereiscontrafold = %s\n", whereiscontrafold );
--argc;
goto nextoption;
default:
fprintf( stderr, "illegal option %c\n", c );
argc = 0;
break;
}
}
nextoption:
;
}
if( argc != 0 )
{
fprintf( stderr, "options: Check source file !\n" );
exit( 1 );
}
}
int main( int argc, char *argv[] )
{
static char com[10000];
static int *nlen;
int left, right;
int res;
static char **name, **seq, **nogap;
static int **gapmap;
static int *order;
int i, j;
FILE *infp;
RNApair ***pairprob;
RNApair **alnpairprob;
RNApair *pairprobpt;
RNApair *pt;
int *alnpairnum;
double prob;
int adpos;
arguments( argc, argv );
if( inputfile )
{
infp = fopen( inputfile, "r" );
if( !infp )
{
fprintf( stderr, "Cannot open %s\n", inputfile );
exit( 1 );
}
}
else
infp = stdin;
if( !whereiscontrafold )
whereiscontrafold = "";
getnumlen( infp );
rewind( infp );
if( dorp != 'd' )
{
fprintf( stderr, "nuc only\n" );
exit( 1 );
}
seq = AllocateCharMtx( njob, nlenmax*2+1 );
nogap = AllocateCharMtx( njob, nlenmax*2+1 );
gapmap = AllocateIntMtx( njob, nlenmax*2+1 );
order = AllocateIntVec( njob );
name = AllocateCharMtx( njob, B+1 );
nlen = AllocateIntVec( njob );
pairprob = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
alnpairprob = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
alnpairnum = AllocateIntVec( nlenmax );
for( i=0; i<nlenmax; i++ ) alnpairnum[i] = 0;
readData_pointer( infp, name, nlen, seq );
fclose( infp );
for( i=0; i<njob; i++ )
{
pairprob[i] = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
for( j=0; j<nlenmax; j++ )
{
pairprob[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
pairprob[i][j][0].bestpos = -1;
pairprob[i][j][0].bestscore = -1.0;
}
unknown_n( nogap[i], seq[i] );
order[i] = i;
}
for( j=0; j<nlenmax; j++ )
{
alnpairprob[j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
alnpairprob[j][0].bestpos = -1;
alnpairprob[j][0].bestscore = -1.0;
}
constants( njob, seq );
fprintf( stderr, "running contrafold\n" );
for( i=0; i<njob; i++ )
{
fprintf( stderr, "%d / %d\n", i+1, njob );
commongappick_record( 1, nogap+i, gapmap[i] );
infp = fopen( "_contrafoldin", "w" );
fprintf( infp, ">in\n%s\n", nogap[i] );
fclose( infp );
#if 0 // contrafold v1
sprintf( com, "env PATH=%s contrafold predict _contrafoldin --posteriors 0.01 > _contrafoldout", whereiscontrafold );
#else // contrafold v2
sprintf( com, "env PATH=%s contrafold predict _contrafoldin --posteriors 0.01 _contrafoldout", whereiscontrafold );
#endif
res = system( com );
if( res )
{
fprintf( stderr, "error in contrafold\n" );
fprintf( stderr, "=================================================================\n" );
fprintf( stderr, "=================================================================\n" );
fprintf( stderr, "==\n" );
fprintf( stderr, "== This version of MAFFT supports CONTRAfold v2.02.\n" );
fprintf( stderr, "== If you have a lower version of CONTRAfold installed in the\n" );
fprintf( stderr, "== %s directory,\n", whereiscontrafold );
fprintf( stderr, "== please update it!\n" );
fprintf( stderr, "==\n" );
fprintf( stderr, "=================================================================\n" );
fprintf( stderr, "=================================================================\n" );
exit( 1 );
}
infp = fopen( "_contrafoldout", "r" );
readcontrafold( infp, pairprob[i], nlenmax );
fclose( infp );
fprintf( stdout, ">%d\n", i );
outcontrafold( stdout, pairprob[i], nlenmax );
}
for( i=0; i<njob; i++ )
{
for( j=0; j<nlen[i]; j++ ) for( pairprobpt=pairprob[i][j]; pairprobpt->bestpos!=-1; pairprobpt++ )
{
left = gapmap[i][j];
right = gapmap[i][pairprobpt->bestpos];
prob = pairprobpt->bestscore;
for( pt=alnpairprob[left]; pt->bestpos!=-1; pt++ )
if( pt->bestpos == right ) break;
if( pt->bestpos == -1 )
{
alnpairprob[left] = (RNApair *)realloc( alnpairprob[left], (alnpairnum[left]+2) * sizeof( RNApair ) );
adpos = alnpairnum[left];
alnpairnum[left]++;
alnpairprob[left][adpos].bestscore = 0.0;
alnpairprob[left][adpos].bestpos = right;
alnpairprob[left][adpos+1].bestscore = -1.0;
alnpairprob[left][adpos+1].bestpos = -1;
pt = alnpairprob[left]+adpos;
}
else
adpos = pt-alnpairprob[left];
pt->bestscore += prob;
if( pt->bestpos != right )
{
fprintf( stderr, "okashii!\n" );
exit( 1 );
}
// fprintf( stderr, "adding %d-%d, %f\n", left, right, prob );
}
}
return( 0 );
#if 0
fprintf( stdout, "result=\n" );
for( i=0; i<nlenmax; i++ ) for( pairprobpt=alnpairprob[i]; pairprobpt->bestpos!=-1; pairprobpt++ )
{
pairprobpt->bestscore /= (double)njob;
left = i;
right = pairprobpt->bestpos;
prob = pairprobpt->bestscore;
fprintf( stdout, "%d-%d, %f\n", left, right, prob );
}
return( 0 );
#endif
}
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