int main(int argc,char **argv)
{
int i,nseqs;
char infile[FILENAMELEN+1];
char outfile[FILENAMELEN+1];
ALN mult_aln;
OPT opt;
if(argc!=3) {
fprintf(stderr,"Usage: %s input_aln output_aln\n",argv[0]);
exit(1);
}
strcpy(infile,argv[1]);
strcpy(outfile,argv[2]);
init_options(&opt);
(*opt.alnout_opt).output_clustal=FALSE;
(*opt.alnout_opt).output_gcg=TRUE;
/* read in the sequences */
seq_input(infile,opt.explicit_type,FALSE,&mult_aln);
if(mult_aln.nseqs<=0) {
fprintf(stderr,"ERROR: No sequences in %s\n",infile);
exit(1);
}
nseqs=mult_aln.nseqs;
/* write out the sequences */
strcpy((*opt.alnout_opt).gcg_outname, outfile);
for (i=0;i<mult_aln.nseqs;i++) mult_aln.seqs[i].output_index = i;
if(!open_alignment_output(infile,opt.alnout_opt)) exit(1);
create_alignment_output(mult_aln,*opt.alnout_opt);
}
static void format_options_menu(void) /* format of alignment output */
{
sint i;
sint length = 0;
char path[FILENAMELEN+1];
int catchint;
catchint = signal(SIGINT, SIG_IGN) != SIG_IGN;
if (catchint) {
if (setjmp(jmpbuf) != 0)
fprintf(stdout,"\n.. Interrupt\n");
#ifdef UNIX
if (signal(SIGINT,jumper) == BADSIG)
fprintf(stdout,"Error: signal\n");
#else
if (signal(SIGINT,SIG_DFL) == (void*)BADSIG)
fprintf(stdout,"Error: signal\n");
#endif
}
while(TRUE) {
fprintf(stdout,"\n\n\n");
fprintf(stdout," ********* Format of Alignment Output *********\n");
fprintf(stdout,"\n\n");
fprintf(stdout," F. Toggle FASTA format output = %s\n\n",
(!output_fasta) ? "OFF" : "ON");
fprintf(stdout," 1. Toggle CLUSTAL format output = %s\n",
(!output_clustal) ? "OFF" : "ON");
fprintf(stdout," 2. Toggle NBRF/PIR format output = %s\n",
(!output_nbrf) ? "OFF" : "ON");
fprintf(stdout," 3. Toggle GCG/MSF format output = %s\n",
(!output_gcg) ? "OFF" : "ON");
fprintf(stdout," 4. Toggle PHYLIP format output = %s\n",
(!output_phylip) ? "OFF" : "ON");
fprintf(stdout," 5. Toggle NEXUS format output = %s\n",
(!output_nexus) ? "OFF" : "ON");
fprintf(stdout," 6. Toggle GDE format output = %s\n\n",
(!output_gde) ? "OFF" : "ON");
fprintf(stdout," 7. Toggle GDE output case = %s\n",
(!lowercase) ? "UPPER" : "LOWER");
fprintf(stdout," 8. Toggle CLUSTALW sequence numbers = %s\n",
(!cl_seq_numbers) ? "OFF" : "ON");
fprintf(stdout," 9. Toggle output order = %s\n\n",
(output_order==0) ? "INPUT FILE" : "ALIGNED");
fprintf(stdout," 0. Create alignment output file(s) now?\n\n");
fprintf(stdout," T. Toggle parameter output = %s\n",
(!save_parameters) ? "OFF" : "ON");
fprintf(stdout," R. Toggle sequence range numbers = %s\n",
(!seqRange) ? "OFF" : "ON");
fprintf(stdout,"\n");
fprintf(stdout," H. HELP\n\n\n");
getstr("Enter number (or [RETURN] to exit)",lin2);
if(*lin2 == EOS) return;
switch(toupper(*lin2)) {
case '1':
output_clustal ^= TRUE;
break;
case '2':
output_nbrf ^= TRUE;
break;
case '3':
output_gcg ^= TRUE;
break;
case '4':
output_phylip ^= TRUE;
break;
case '5':
output_nexus ^= TRUE;
break;
case '6':
output_gde ^= TRUE;
break;
case '7':
lowercase ^= TRUE;
break;
case '8':
cl_seq_numbers ^= TRUE;
break;
case '9':
if (output_order == INPUT) output_order = ALIGNED;
else output_order = INPUT;
break;
case 'F':
output_fasta ^= TRUE;
break;
case 'R':
seqRange ^= TRUE;
break;
case '0': /* DES */
if(empty) {
error("No sequences loaded");
break;
}
get_path(seqname,path);
if(!open_alignment_output(path)) break;
create_alignment_output(1,nseqs);
break;
case 'T': save_parameters ^= TRUE;
break;
case '?':
case 'H':
get_help('5');
break;
default:
fprintf(stdout,"\n\nUnrecognised Command\n\n");
break;
}
}
}
int main(int argc, char **argv)
{
FILE *ofd,*ifd;
ALN mult_aln;
OPT opt;
char infile[FILENAMELEN+1];
char outfile[FILENAMELEN+1];
int nseqs;
int i,j,l,n,ires;
int err,ix,ntot;
float min_nn,nn;
float tmp;
Boolean eof,found;
if(argc!=3 && argc!=7 && argc!=8) {
usage(argv[0]);
return 0;
}
strcpy(infile,argv[1]);
strcpy(outfile,argv[2]);
/* open the matrix file */
verbose=FALSE;
if(argc==3) {
get_default_matrix();
go=0.0;
ge=0.1;
egap=0.0;
}
else {
if(argc==8) verbose=TRUE;
if((ifd=fopen(argv[3],"r"))==NULL) {
fprintf(stderr,"Cannot open matrix file [%s]",argv[3]);
return 0;
}
err=readmatrix(ifd);
if(err<=0) {
fprintf(stderr,"Error: bad matrix in %s\n",argv[3]);
return 0;
}
go=atof(argv[4]);
ge=atof(argv[5]);
egap=atof(argv[6]);
}
init_options(&opt);
(*opt.alnout_opt).output_clustal=FALSE;
(*opt.alnout_opt).output_relacs=TRUE;
/* read in the sequences */
seq_input(infile,opt.explicit_type,FALSE,&mult_aln);
if(mult_aln.nseqs<=0) {
error("No sequences in %s\n",infile);
exit(1);
}
nseqs=mult_aln.nseqs;
/* remove the gaps */
seqlength=0;
useqlen_array=(int *)ckalloc((nseqs+1)*sizeof(int));
for(i=0;i<nseqs;i++) {
if(mult_aln.seqs[i].len>seqlength) seqlength=mult_aln.seqs[i].len;
l=0;
for(j=0;j<mult_aln.seqs[i].len;j++)
if(isalpha(mult_aln.seqs[i].data[j])) {
l++;
}
useqlen_array[i]=l;
}
maxlen=0;
for(i=0;i<nseqs;i++)
if(useqlen_array[i]>maxlen) maxlen=useqlen_array[i];
minlen=10000;
for(i=0;i<nseqs;i++)
if(useqlen_array[i]<minlen) minlen=useqlen_array[i];
/* remove any column score data that already exists in the input file */
/*if (mult_aln.ncol_scores==1)
ckfree(mult_aln.col_score[0].data);*/
ix=mult_aln.ncol_scores;
mult_aln.col_score[ix].data=(sint *)ckalloc((seqlength+1)*sizeof(sint));
mult_aln.ncol_scores=ix+1;
/* calculate some simple statistics */
pcid=(float **)ckalloc((nseqs+1)*sizeof(float *));
for(i=0;i<nseqs;i++)
pcid[i]=(float *)ckalloc((nseqs+1)*sizeof(float));
for(i=0;i<nseqs;i++) {
for(j=i+1;j<nseqs;j++) {
pcid[j][i]=pcid[i][j]=pcidentity(mult_aln,i,j);
}
}
/* find the nearest neighbor for each sequence */
min_nn=1.0;
for(i=0;i<nseqs;i++) {
nn=0.0;
for(j=0;j<nseqs;j++) {
if(i!=j && pcid[i][j]>nn) nn=pcid[i][j];
}
if(nn<min_nn) min_nn=nn;
}
seqweight=(float **)ckalloc((nseqs+1)*sizeof(float *));
for(i=0;i<nseqs;i++)
seqweight[i]=(float *)ckalloc((nseqs+1)*sizeof(float));
for(i=0;i<nseqs;i++)
for(j=i;j<nseqs;j++) {
seqweight[j][i]=seqweight[i][j]=1.0-pcid[i][j];
}
fragment=(Boolean *)ckalloc((nseqs+1)*sizeof(Boolean));
/* calculate pairwise alignment scores using k-tuple scores */
qpw_id=(float **)ckalloc((nseqs+1)*sizeof(float *));
for(i=0;i<nseqs;i++)
qpw_id[i]=(float *)ckalloc((nseqs+1)*sizeof(float));
for(i=0,n=0;i<nseqs;i++)
for(j=i+1;j<nseqs;j++) {
qpw_id[i][j]=100.0*pcid[i][j];
if(qpw_id[i][j]<60) {
qpw_id[i][j]=show_pair(mult_aln,i,j);
}
if(qpw_id[i][j]>40) {
tmp=(float)useqlen_array[i]/(float)useqlen_array[j];
if(tmp<0.8) fragment[i]=TRUE;
else if(tmp>1.25) fragment[j]=TRUE;
}
n++;
}
/*if(verbose)
for(i=0;i<nseqs;i++)
if(fragment[i]) fprintf(stdout,"%s fragment %s\n",argv[1],names[i]);*/
/* calculate sequence groups and keep first sequence in each group for processing */
use_seq=(int *)ckalloc((nseqs+1)*sizeof(int));
for(i=0;i<nseqs;i++)
use_seq[i]=2;
query=0;
seqgroup=(int *)ckalloc((nseqs+1)*sizeof(int));
groupseed=(int *)ckalloc((nseqs+1)*sizeof(int));
calc_groups(query,0.7,nseqs,pcid,seqgroup,groupseed);
if(ngroups<=0) {
fprintf(stderr,"Error: problem with sequence grouping\n");
exit(1);
}
for(j=0;j<nseqs;j++) use_seq[j]=(-1);
for(i=0;i<ngroups;i++) {
j=groupseed[i];
use_seq[j]=2;
}
for(i=0;i<nseqs;i++)
ckfree(pcid[i]);
ckfree(pcid);
ckfree(groupseed);
ckfree(seqgroup);
qpw=(float *)ckalloc((ngroups*ngroups+1)*sizeof(float));
for(i=0,n=0;i<nseqs;i++)
if(use_seq[i]>1)
for(j=i+1;j<nseqs;j++)
if(use_seq[j]>1)
qpw[n++]=qpw_id[i][j];
for(i=0;i<nseqs;i++)
ckfree(qpw_id[i]);
ckfree(qpw_id);
/* sort the pairwise k-tuple scores into ascending order */
sort_scores(qpw,0,n-1);
/* calculate the scores for the gaps */
gop=(float **)ckalloc((nseqs+1)*sizeof(float *));
for(i=0;i<nseqs;i++)
gop[i]=(float *)ckalloc((nseqs+1)*sizeof(float));
gep=(float **)ckalloc((nseqs+1)*sizeof(float *));
for(i=0;i<nseqs;i++)
gep[i]=(float *)ckalloc((nseqs+1)*sizeof(float));
egp=(float **)ckalloc((nseqs+1)*sizeof(float *));
for(i=0;i<nseqs;i++)
egp[i]=(float *)ckalloc((nseqs+1)*sizeof(float));
for(i=0;i<nseqs;i++)
if(use_seq[i]>1)
for(j=i+1;j<nseqs;j++)
if(use_seq[j]>1)
score_gaps(mult_aln,i,j);
calc_md(&mult_aln,ix);
for(i=0,ntot=0;i<nseqs;i++)
if(use_seq[i]>1) {
ntot++;
}
tmp=set_mdcutoff(ntot,q1);
normd_rs/=tmp;
tmp=1.0;
norm_md/=tmp;
mult_aln.alnscore=norm_md;
mult_aln.validalnscore=TRUE;
if(!verbose) {
fprintf(stdout,"%s\t%.3f\n",argv[1],norm_md);
/*fprintf(stdout,"%.3f\n",norm_md);*/
} else {
/*fprintf(stdout,"%s %.3f %.3f %.3f %.3f %.3f %.3f %d %d %d\n",
argv[1],norm_md,normd_rs,col,max_colscore,gap_extscore*0.1,q1,nseqs,minlen,maxlen);*/
fprintf(stdout,"FILE %s\n",argv[1]);
fprintf(stdout,"norMD %.3f\n",norm_md);
/*fprintf(stdout,"norMD_of %.3f\n",norm_md);
fprintf(stdout,"norMD_rs %.3f\n",normd_rs);*/
fprintf(stdout,"NSEQS %d\n",nseqs);
fprintf(stdout,"MD %.3f\n",col);
fprintf(stdout,"maxMD %.3f\n",max_colscore);
fprintf(stdout,"GOP %.3f\n",gap_openscore);
fprintf(stdout,"GEP %.3f\n",gap_extscore);
fprintf(stdout,"LQR %.3f\n",q1);
}
for(i=0;i<nseqs;i++)
ckfree(gop[i]);
ckfree(gop);
for(i=0;i<nseqs;i++)
ckfree(gep[i]);
ckfree(gep);
for(i=0;i<nseqs;i++)
ckfree(egp[i]);
ckfree(egp);
for(i=0;i<nseqs;i++)
ckfree(seqweight[i]);
ckfree(seqweight);
ckfree(qpw);
ckfree(use_seq);
ckfree(fragment);
ckfree(useqlen_array);
/* write out the sequences */
strcpy(opt.alnout_opt->relacs_outname,outfile);
if(!open_alignment_output(outfile,opt.alnout_opt)) exit(1);
create_alignment_output(mult_aln,*opt.alnout_opt);
return 0;
}
