+++ /dev/null
-#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;
- float 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:%f", &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;
- float 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 /= (float)njob;
- left = i;
- right = pairprobpt->bestpos;
- prob = pairprobpt->bestscore;
- fprintf( stdout, "%d-%d, %f\n", left, right, prob );
- }
-
- return( 0 );
-#endif
-}
git://source.jalview.org / jabaws.git / blobdiff