void ramen_load_motifs() {
BOOLEAN_T read_file = FALSE;
MREAD_T *mread;
ARRAYLST_T* read_motifs;
int num_motifs_before_rc;
int i;
int j;
memset(&motifs, 0, sizeof(ramen_motifs_t));
read_motifs = arraylst_create();
for (i = 0; i < args.number_motif_files; i++) {
mread = mread_create(args.motif_filenames[i], OPEN_MFILE);
if (args.bg_format == FILE_BG) {
mread_set_bg_source(mread, args.bg_filename);
} else {
mread_set_background(mread, motifs.bg_freqs);
}
mread_set_pseudocount(mread, args.pseudocount);
mread_load(mread, read_motifs);
if (!(motifs.bg_freqs)) motifs.bg_freqs = mread_get_background(mread);
mread_destroy(mread);
}
// reverse complement the originals adding to the original read in list
num_motifs_before_rc = arraylst_size(read_motifs);
add_reverse_complements(read_motifs);
motifs.num = arraylst_size(read_motifs);
//Allocate array for the motifs
motif_list_to_array(read_motifs, &(motifs.motifs), &(motifs.num));
//free the list of motifs
free_motifs(read_motifs);
// check reverse complements.
assert(motifs.num / 2 == num_motifs_before_rc);
// reset motif count to before rev comp
motifs.num = num_motifs_before_rc;
//Now, we need to convert the motifs into odds matrices if we're doing that kind of scoring
for (i=0;i<2*motifs.num;i++) {
convert_to_odds_matrix(motif_at(motifs.motifs, i), motifs.bg_freqs);
}
}
MaxResults suboptSampler(Model B, PoSition **Pos, SimTime *S)
{
int **nNumMotifs,
**startPos, /* startPos[MotifType][motifnum] */
i, j, seed_run = 0, t, k;
int maxnum; /* maximum number of motif in one type motif */
register Mlist M;
MaxResults maxData, locMax;
RPType RP;
IPtype IP; /* for quick access of input data */
PoSition *Pos_t; /* Pos_t=Pos[t] */
int n; /* BT 2/7/97 */
int nPos;
int sum;
double dCurrProb;
#ifdef _MPI_
MPI_Status status;
double dTempInfo[4];
#endif
IP=B->IP;
RP = B->RP;
init_maxdata(&maxData);
init_maxdata(&locMax);
BeginTime(S);
#ifdef _MPI_
if( ! IP->is_defined[cl_hm] )
{
/* get the go ahead to start */
Gibbs_MPI_Recv( B, &dTempInfo, 4, MPI_DOUBLE, MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD,
&status );
if( status.MPI_TAG == G_MPI_DONE )
return maxData;
if( IP->is_defined[cl_X] && B->AN->bExchange )
{
B->AN->currTemp = dTempInfo[0];
B->AN->dMinTemp = B->AN->currTemp;
B->AN->dMaxTemp = B->AN->currTemp;
PrintTempOut(IP->Datafiles->mpiTemp_fpt, "currTemp = %f maxTemp = %f minTemp = %f\n",
B->AN->currTemp, B->AN->dMaxTemp, B->AN->dMinTemp );
}
}
#endif
/* save the inital number of motifs */
for(t = 0; t < IP->nNumMotifTypes; t++) /* BT 2/7/97 */
{
RP->nPriorMotifSites[t][FORWARD] = IP->nNumMotifs[t][FORWARD];
RP->nPriorMotifSites[t][REVERSE] = IP->nNumMotifs[t][REVERSE];
}
/* copy the original counts into current counts */
copy_counts(B);
nNumMotifs = copy_motif_num(IP);
zero_motifs(IP); /* set motif count to zero */
/* If not running Wilcox test initialize random number gerator. */
/* Wilcox already did this */
if( ! IP->is_defined[cl_l] ) /* BT 7/23/97 */
sRandom(B, IP->lSeedVal);
/* calculate the probability of NULL model */
/* IP->dnull_map = CalcMapProb(B, IP->is_defined[cl_R]); */
IP->dnull_map = CalcNullMap(B); /* 2/16/2001 */
reset_motif_num(nNumMotifs,IP);
/* mark all possible motif sites */
if( ! IP->inCentroidAlign )
set_indicator_vector(Pos, B->Seq, B);
maxnum = findMaxNumMotif(IP);
if( IP->is_defined[cl_E] ||
RP->nUseSpacingProb || IP->is_defined[cl_T] ) /* BT 11/20/2000 */
{
CountAlignments( B, Pos );
SaveAlignmentCounts( B );
}
/* allocate space for start positions of motifs */
NEWP(startPos,IP->nNumMotifTypes, int);
for(i = 0; i <IP->nNumMotifTypes ; i++)
NEW(startPos[i],maxnum, int);
/* Loop through for a number of different seeds */
while(seed_run++ < IP->nSeeds)
{
if( IP->is_defined[cl_X] )
{
/* if( ! B->AN->bExchange )
B->AN->currTemp = B->AN->dMaxTemp; */
if( ! IP->is_defined[cl_Z] )
printf( "Current temperature: %7.2f\n", B->AN->currTemp );
}
IP->nSeedRun = seed_run;
if(!IP->is_defined[cl_F])
initMask(B);
if( IP->is_defined[cl_X] )
init_maxdata( &(B->AN->results[seed_run]) );
/* initialize the Pos */
for(t=0;t<IP->nNumMotifTypes;t++)
{
Pos_t=Pos[t];
for(i = 0; i < IP->nSeqLen; i++)
{
Pos_t[i].nInMotif=FALSE;
Pos_t[i].nMotifStartPos=FALSE;
}
}
for( t= 0; t < IP->nNumMotifTypes; t++ ) /* BT 5/23/97 */
{
IP->nMotifLen[t] = IP->nInputMotifLen[t]; /* restore original lengths */
SetPossibleSites( B, t ); /* restore original site count */
}
if( IP->is_defined[cl_d] && ! IP->inCentroidAlign )
set_indicator_vector(Pos, B->Seq, B);
if( ! IP->site_samp ) /* BT 7/16/97 */
set_posterior_prob(IP, B->C); /* Set initial posterior prob */
/* random select a set of motifs */
if( ! IP->is_defined[cl_V] ) /* BT 04/16/03 */
{
if( B->InitPos == NULL || seed_run > 1 )
{
if( IP->is_defined[cl_A] )
{
set_posterior_prob(IP, B->C);
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
IP->nNumMotifs[t][FORWARD] = 0;
IP->nNumMotifs[t][REVERSE] = 0;
}
}
set_random_sequences(B, Pos, startPos); /* set alignment &*/
}
else
{
SetInitSequences( B, Pos, startPos ); /* BT 8/5/98 */
set_posterior_prob(IP, B->First);
if( RP->bUsePosMatrix )
InitializePosMatrix( B );
else if( RP->bUseTrans )
InitializeTransMatrix( B );
}
}
else
{
if( B->InitPos == NULL )
{
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
IP->nNumMotifs[t][FORWARD] = 0;
IP->nNumMotifs[t][REVERSE] = 0;
}
}
else
{
SetInitSequences( B, Pos, startPos );
set_counts( B ); /* BT 10/23/03 */
set_posterior_prob(IP, B->First);
}
set_posterior_prob(IP, B->C);
}
reset_counts(B, startPos, Pos); /* its counts */
if( B->InitPos != NULL && seed_run == 1 )
{
RP->dInitProb = CalcMapProb( B, IP->is_defined[cl_R] );
if( ! IP->inCentroidAlign )
{
fprintf( IP->Datafiles->out_fpt, "seed = %d Initial MAP = %.5f sites = %d \n",
IP->nSeedRun,
RP->dInitProb,
TotalNumMotifs( B ));
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
fprintf(IP->Datafiles->out_fpt,
"Motif %d Map = %.5f Frag = %.5f\n", t,
CalcMotifMap(B, t, IP->is_defined[cl_R]),
CalcMotifFragMap(B, t, IP->is_defined[cl_R]) );
}
}
#ifdef _MPI_
PrintTempOut( IP->Datafiles->mpiTemp_fpt,
"rank = %d process = %d seed = %d Initial MAP = %.5f sites = %d\n",
IP->nRank,
IP->nMPIProcesses,
IP->nSeedRun,
RP->dInitProb,
TotalNumMotifs( B ) );
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
PrintTempOut( IP->Datafiles->mpiTemp_fpt,
"%d Motif = %.5f Frag = %.5f\n", t,
CalcMotifMap(B, t, IP->is_defined[cl_R]),
CalcMotifFragMap(B, t, IP->is_defined[cl_R]) );
}
PrintTempOut( IP->Datafiles->mpiTemp_fpt,
"Bkgnd = %.5f Beta = %.5f Null = %.5f\n",
CalcBkgndMap(B, IP->is_defined[cl_R]),
CalcBetaMap( B, IP->is_defined[cl_R]),
IP->dnull_map );
#else
fprintf( stdout, "seed = %d Initial MAP = %.5f sites = %d\n",
IP->nSeedRun,
B->RP->dInitProb,
TotalNumMotifs( B ) );
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
fprintf( stdout,
"%d Motif = %.5f Frag = %.5f\n", t,
CalcMotifMap(B, t, IP->is_defined[cl_R]),
CalcMotifFragMap(B, t, IP->is_defined[cl_R]) );
}
fprintf( stdout,
"Bkgnd = %.5f Beta = %.5f Seq = %.5f Null = %.5f\n",
CalcBkgndMap(B, IP->is_defined[cl_R]),
CalcBetaMap( B, IP->is_defined[cl_R]),
CalcSitePerSeqMap( B ),
IP->dnull_map );
#endif
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
fprintf( stdout,
"-----------------------------------------------------------\n" );
fprintf( stdout, " MOTIF %c\n\n", (char)(97 + t));
DumpMotifPositions( t, B, Pos, stdout );
fprintf( stdout, "%d sites\n", NUMMOTIFS( IP->nNumMotifs[t]) );
}
fflush( stdout );
}
/* create a motif element list */
M = set_motif_info(IP, startPos, B->Seq);
#ifdef _DEBUG_
/* ==================================================================== */
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
fprintf( stdout,
"-----------------------------------------------------------\n" );
fprintf( stdout, " MOTIF %c\n\n", (char)(97 + t));
DumpMotifPositions( t, B, Pos, stdout );
fprintf( stdout, "%d sites\n", NUMMOTIFS( IP->nNumMotifs[t]) );
DumpCounts( B, t, stdout );
fflush( stdout );
}
/* ==================================================================== */
#endif
if( ! IP->is_defined[cl_Z] )
{
put_prior(B);
fprintf(stdout, "\r** %d **\n", seed_run);
fflush( stdout ); /* BT 9/19/97 */
}
if(seed_run > 1)
{
RestoreAlignmentCounts( B );
if(IP->site_samp)
locMax = site_sampler(B, Pos, M);
else if( IP->is_defined[cl_bayes] )
locMax = bayes_sampler(B, Pos, M, seed_run);
else if( IP->is_defined[cl_E] )
locMax = rsite_sampler(B, Pos, M, seed_run);
else
locMax = motif_sampler(B,Pos,M);
if( IP->is_defined[cl_X] )
CopyMaxResults( &(B->AN->results[seed_run]), &locMax, B );
dCurrProb = locMax.dProbability;
if(locMax.dProbability > maxData.dProbability)
{
/* Check to see if current run is max */
free_maxdata(&maxData, IP);
maxData = locMax;
maxData.nSuboptSeed = seed_run;
if( (! IP->is_defined[cl_Z]) && IP->is_defined[cl_opt] )
print_maxData(IP->nNumMotifTypes, maxData);
}
else
free_maxdata(&locMax, IP);
}
else
{ /* Set Maximum first time through */
if(IP->site_samp)
maxData = site_sampler(B, Pos, M);
else if( IP->is_defined[cl_bayes] )
maxData = bayes_sampler(B, Pos, M, seed_run);
else if( IP->is_defined[cl_E] )
maxData = rsite_sampler(B, Pos, M, seed_run);
else
maxData = motif_sampler(B,Pos,M);
dCurrProb = maxData.dProbability;
maxData.nSuboptSeed = seed_run;
if( IP->is_defined[cl_X] )
CopyMaxResults( &(B->AN->results[seed_run]), &maxData, B );
if( (! IP->is_defined[cl_Z]) && IP->is_defined[cl_opt] )
print_maxData(IP->nNumMotifTypes, maxData);
}
reset_motif_num(nNumMotifs, IP);
copy_counts(B); /* Counts w/o motifs */
free_motifs(B, M);
#ifdef _MPI_
if( IP->is_defined[cl_hm] )
{
if( seed_run == IP->nSeeds )
SendSuboptMsg( B, G_MPI_SUBOPT_DONE, seed_run );
else
SendSuboptMsg( B, G_MPI_SEED_DONE, seed_run );
}
else
{
dTempInfo[1] = dCurrProb;
dTempInfo[3] = 0;
if( IP->is_defined[cl_opt] )
{
for(t = 0; t < IP->nNumMotifTypes; t++)
{
dTempInfo[3] += (double) maxData.nNumMotifs[t];
}
}
Gibbs_MPI_Send( B, dTempInfo, 4, MPI_DOUBLE, 0, G_MPI_DATA, MPI_COMM_WORLD );
}
Gibbs_MPI_Recv( B, dTempInfo, 4, MPI_DOUBLE, 0, MPI_ANY_TAG, MPI_COMM_WORLD,
&status );
if( status.MPI_TAG == G_MPI_DONE )
{
PrintTempOut( IP->Datafiles->mpiTemp_fpt, "Received MPI_DONE signal\n" );
break;
}
else if( status.MPI_TAG == G_MPI_FINISH )
{
PrintTempOut( IP->Datafiles->mpiTemp_fpt, "Received subopt end signal\n" );
break;
}
#endif
}/* end of while loop, at this time we have MaxData */
FREEP(startPos,IP->nNumMotifTypes );
if(!IP->is_defined[cl_F] && maxData.F)
{
for(t = 0; t < IP->nNumMotifTypes; t++) /* BT 2/7/97 */
{
for(n = 0; n < B->F->nMaxLen[t]; n++)
B->F->nColMask[t][n] = maxData.F->nColMask[t][n];
B->F->FragWidth[t] = maxData.F->FragWidth[t];
for( n = 0; n < IP->nMotifLen[t]; n++ )
B->F->fragPos[t][n] = maxData.F->fragPos[t][n];
}
}
for(t = 0; t < IP->nNumMotifTypes; t++)
{ /* Add in motifs */
if( maxData.nMotifLen )
IP->nMotifLen[t] = maxData.nMotifLen[t];
/* Reset Pos in case width changed */
if( ! IP->inCentroidAlign )
set_indicator_vector(Pos, B->Seq, B); /* BT 9/12/97 */
if( maxData.nNumMotifs )
{
for(i = 0; i < maxData.nNumMotifs[t]; i++) /* from the maximum */
adjust_counts(B, ADD, maxData.nMotifLoc[i][t], /* alignment */
t, maxData.RevComp[i][t]);
}
}
if( maxData.nNumMotifs )
{
setMotifNum(IP, maxData); /* BT 5/30/97 */
}
if( IP->is_defined[cl_u] )
print_info(B, maxData, TRUE, SUBOPT); /* BT 3/19/97 */
if( IP->is_defined[cl_d] && IP->is_defined[cl_q] )
GetWidthCounts( B );
FREEP(nNumMotifs, IP->nNumMotifTypes);
free(nNumMotifs);
if( IP->is_defined[cl_Q] ) /* BT 3/27/98 */
{
fprintf( IP->Datafiles->occur_fpt, "seq pos pos2 motif count\n" );
for( i = 0; i < IP->nNumSequences; i++ )
{
for( j = 0; j < SequenceLength( B, i ); j++ )
{
nPos = SequenceStartPos( B, i ) + j;
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
for( sum = 0, k = 1; k <= IP->nSeeds; k++ )
{
sum += IP->nAlignCnts[k][t][i][j];
}
fprintf( IP->Datafiles->occur_fpt, "%5d %5d %5d %5d %5d\n",
i, j, nPos, t, sum );
}
}
fflush( IP->Datafiles->occur_fpt );
}
}
if( ! IP->is_defined[cl_Z] && ! IP->is_defined[cl_nopt] )
printf( "Max subopt MAP found on seed %d\n", maxData.nSuboptSeed );
return maxData;
}
void generate_ceq_logos(char *meme_path, char *output_dir) {
int i, dir_len, prefix_len, path_len;
ARRAY_T *background;
BOOLEAN_T has_reverse_strand;
char *path, *alphabet;
double logo_height, logo_width;
ARRAYLST_T *motifs;
MOTIF_T *motif;
motifs = arraylst_create();
logo_height = LOGOHEIGHT;
//make the path
dir_len = strlen(output_dir);
prefix_len = strlen(LOGO_PREFIX);
path_len = dir_len + 1 + prefix_len + MAX_MOTIF_ID_LENGTH + 1;
path = malloc(sizeof(char)*path_len);
strncpy(path, output_dir, path_len);
if (path[dir_len-1] != '/') {
path[dir_len] = '/';
path[++dir_len] = '\0';
}
strncpy(path+dir_len, LOGO_PREFIX, path_len - dir_len);
// Read all motifs into an array.
read_meme_file2(meme_path,
NULL, // bg file name
DEFAULT_PSEUDOCOUNTS,
REQUIRE_PSPM,
motifs,
NULL,//motif occurrences
&has_reverse_strand,
&background);
// global alphabet is set by read_meme_file
alphabet = get_alphabet(FALSE);
if (create_output_directory(output_dir, TRUE, (verbosity >= NORMAL_VERBOSE))) {
// Failed to create output directory.
exit(1);
}
for(i = 0; i < arraylst_size(motifs); i++) {
motif = (MOTIF_T*)arraylst_get(i, motifs);
logo_width = get_motif_length(motif);
if (logo_width > MAXLOGOWIDTH) logo_width = MAXLOGOWIDTH;
copy_and_sanatise_name(path+(dir_len+prefix_len), get_motif_id(motif), path_len - (dir_len + prefix_len));
CL_create2(
motif, // motif
"", // no title
NULL, // no second motif
"", // no x-axis label
FALSE, // no error bars
FALSE, // ssc
logo_height, // logo height (cm)
logo_width, // logo width (cm)
alphabet, // alphabet
0, // no offset to second motif
path, // output file path
"MEME (no SSC)" // program name
);
}
free_motifs(motifs);
free_array(background); // not used
free(path);
}