FILE * open_output_file(char *in_name, char *prompt, char *file_extension, char *out_name)
{
char temp[FILENAMELEN+1];
char path[FILENAMELEN+1];
char local_prompt[MAXLINE];
FILE * file_handle;
/* if the output filename is already specified, just open the file and return */
if (out_name[0]!=EOS) {
file_handle = open_explicit_file(out_name);
return file_handle;
}
}
int main(int argc,char **argv)
{
sint i,j,k,n,s;
sint status;
sint result_type;
char c;
char infile[FILENAMELEN+1];
char treefile[FILENAMELEN+1];
float meanid;
FILE *tree;
sint maxres,*gapptr=NULL;
IN_TREEPTR itree;
double dscore;
double meanscore;
double **tmat;
sint window;
sint block_cutoff;
OPT opt;
if(argc!=2) {
fprintf(stdout,"Usage: %s input_aln\n",argv[0]);
exit(1);
}
strcpy(infile,argv[1]);
init_options(&opt);
/* 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);
}
window=8;
/* count pairwise residue percent identities */
tmat = (double **) ckalloc( (mult_aln.nseqs+1) * sizeof (double *) );
for(i=0;i<mult_aln.nseqs;i++)
tmat[i] = (double *)ckalloc( (mult_aln.nseqs+1) * sizeof (double) );
meanscore=0;
for (i=0,n=0;i<mult_aln.nseqs;i++) {
for (j=i+1;j<mult_aln.nseqs;j++) {
dscore = countid(mult_aln.seqs[i],mult_aln.seqs[j]);
tmat[j][i] = tmat[i][j] = (100.0 - dscore)/100.0;
n++;
meanscore+=dscore;
}
}
meanscore/=(float)n;
/*if(mult_aln.nseqs<100) block_cutoff=8;
else if(mult_aln.nseqs<250) block_cutoff=6;
else*/ block_cutoff=5;
if(meanscore>50) block_cutoff=50;
/* make a tree from the percent identities (used for sequence weighting) */
strcpy(treefile,infile);
strcat(treefile,".ph");
if((tree = open_explicit_file(treefile))==NULL) exit(1);
guide_tree(tree,mult_aln.seqs,mult_aln.nseqs, tmat, QUICKNJ);
itree=(IN_TREEPTR)ckalloc(sizeof(IN_TREE));
status = read_tree(treefile, mult_aln.seqs, 0, mult_aln.nseqs,itree);
for(i=0;i<mult_aln.nseqs;i++)
ckfree(tmat[i]);
ckfree(tmat);
if (status < 0) exit(1);
seq_weight = calc_seq_weights(0,mult_aln.nseqs,itree,FALSE);
free_tree(itree);
remove(treefile);
/* find the start and end positions of each sequence */
is = (sint *)ckalloc((mult_aln.nseqs+1) * sizeof(sint));
ie = (sint *)ckalloc((mult_aln.nseqs+1) * sizeof(sint));
for(s=0;s<mult_aln.nseqs;s++) {
is[s]=0;
ie[s] = mult_aln.seqs[s].len;
for (i=0; i<mult_aln.seqs[s].len; i++) {
c = mult_aln.seqs[s].data[i];
if (!isalpha(c))
is[s]++;
else
break;
}
for (i=mult_aln.seqs[s].len-1; i>=0; i--) {
c = mult_aln.seqs[s].data[i];
if (!isalpha(c))
ie[s]--;
else
break;
}
}
matrix.format=0;
maxres = get_cl_matrix(FALSE, gon250mt, gapptr, TRUE, 100, &matrix);
all_blocks(infile,window,block_cutoff);
}
void create_parameter_output(OPT opt,ALN mult_aln)
{
char parname[FILENAMELEN+1], temp[FILENAMELEN+1];
char path[FILENAMELEN+1];
FILE *parout;
Boolean usemenu;
get_path(mult_aln.filename,path);
strcpy(parname,path);
strcat(parname,"par");
usemenu=get_usemenu();
if(usemenu) {
fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ",
parname);
gets(temp);
if(*temp != EOS)
strcpy(parname,temp);
}
/* create a file with execute permissions first */
remove(parname);
/*
fd = creat(parname, 0777);
close(fd);
*/
if((parout = open_explicit_file(parname))==NULL) return;
fprintf(parout,"clustalw \\\n");
if ((mult_aln.nseqs>0) && (mult_aln.prf1.nseqs<=0)) fprintf(parout,"-infile=%s \\\n",mult_aln.filename);
if (mult_aln.prf1.nseqs>0) fprintf(parout,"-profile1=%s\\\n",mult_aln.prf1.filename);
if (mult_aln.prf2.nseqs>0) fprintf(parout,"-profile2=%s\\\n",mult_aln.prf2.filename);
if (mult_aln.dnaflag == TRUE) fprintf(parout,"-type=dna \\\n");
else fprintf(parout,"-type=protein \\\n");
if (opt.pw_opt->quick_pairalign) {
fprintf(parout,"-quicktree \\\n");
if (!mult_aln.dnaflag) {
fprintf(parout,"-ktuple=%d \\\n",(pint)opt.quickpw_opt->dna_ktup);
fprintf(parout,"-window=%d \\\n",(pint)opt.quickpw_opt->dna_window);
fprintf(parout,"-pairgap=%d \\\n",(pint)opt.quickpw_opt->dna_wind_gap);
fprintf(parout,"-topdiags=%d \\\n",(pint)opt.quickpw_opt->dna_signif);
}
else {
fprintf(parout,"-ktuple=%d \\\n",(pint)opt.quickpw_opt->prot_ktup);
fprintf(parout,"-window=%d \\\n",(pint)opt.quickpw_opt->prot_window);
fprintf(parout,"-pairgap=%d \\\n",(pint)opt.quickpw_opt->prot_wind_gap);
fprintf(parout,"-topdiags=%d \\\n",(pint)opt.quickpw_opt->prot_signif);
}
if (opt.quickpw_opt->percent) fprintf(parout,"/score=percent \\\n");
else fprintf(parout,"-score=absolute \\\n");
}
else {
if (!mult_aln.dnaflag) {
fprintf(parout,"-pwmatrix=%s \\\n",opt.pw_opt->mtrxname);
fprintf(parout,"-pwgapopen=%.2f \\\n",opt.pw_opt->prot_go_penalty);
fprintf(parout,"-pwgapext=%.2f \\\n",opt.pw_opt->prot_ge_penalty);
}
else {
fprintf(parout,"-pwgapopen=%.2f \\\n",opt.pw_opt->dna_go_penalty);
fprintf(parout,"-pwgapext=%.2f \\\n",opt.pw_opt->dna_ge_penalty);
}
}
if (!mult_aln.dnaflag) {
fprintf(parout,"-matrix=%s \\\n",opt.mult_opt->mtrxname);
fprintf(parout,"-gapopen=%.2f \\\n",opt.mult_opt->prot_gap_open);
fprintf(parout,"-gapext=%.2f \\\n",opt.mult_opt->prot_gap_extend);
}
else {
fprintf(parout,"-gapopen=%.2f \\\n",opt.mult_opt->dna_gap_open);
fprintf(parout,"-gapext=%.2f \\\n",opt.mult_opt->dna_gap_extend);
}
fprintf(parout,"-maxdiv=%d \\\n",(pint)opt.mult_opt->divergence_cutoff);
if (!opt.mult_opt->gap_opt->use_endgaps) fprintf(parout,"-endgaps \\\n");
if (!mult_aln.dnaflag) {
if (opt.mult_opt->neg_matrix) fprintf(parout,"-negative \\\n");
if (opt.mult_opt->gap_opt->no_pref_penalties) fprintf(parout,"-nopgap \\\n");
if (opt.mult_opt->gap_opt->no_hyd_penalties) fprintf(parout,"-nohgap \\\n");
if (opt.mult_opt->gap_opt->no_var_penalties) fprintf(parout,"/novgap \\\n");
fprintf(parout,"-hgapresidues=%s \\\n",opt.mult_opt->gap_opt->hyd_residues);
fprintf(parout,"-gapdist=%d \\\n",(pint)opt.mult_opt->gap_opt->gap_dist);
}
else {
fprintf(parout,"-transweight=%.2f \\\n",opt.mult_opt->transition_weight);
}
if (opt.alnout_opt->output_gcg) fprintf(parout,"-output=gcg \\\n");
else if (opt.alnout_opt->output_gde) fprintf(parout,"-output=gde \\\n");
else if (opt.alnout_opt->output_nbrf) fprintf(parout,"-output=pir \\\n");
else if (opt.alnout_opt->output_phylip) fprintf(parout,"-output=phylip \\\n");
if (opt.alnout_opt->output_order==ALIGNED) fprintf(parout,"-outorder=aligned \\\n");
else fprintf(parout,"-outorder=input \\\n");
if (opt.alnout_opt->output_gde)
if (opt.alnout_opt->lowercase) fprintf(parout,"-case=lower \\\n");
else fprintf(parout,"-case=upper \\\n");
fprintf(parout,"-interactive\n");
fclose(parout);
}