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kalignP_main.c
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kalignP_main.c
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/*
kalignP_main.c
Copyright (C) 2010 Nanjiang Shu <[email protected]>
Department of Biochemistry and Biophysics
Stockholm University
Description: multiple sequence alignment supporting external supplied
position specific gap penalties
This software is derived from
Kalign version 2.03, Copyright (C) 2006 Timo Lassmann
http://msa.cgb.ki.se/
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
A copy of this license is in the COPYING file.
*/
#include "kalignP.h"
unsigned int numseq = 0;
unsigned int numprofiles = 0; /*numprofiles = numseq << 1 - 1*/
/*for amino acid sequence, by default*/
/*gpo = (float)54.94941;*/
/*gpe = (float)8.52492;*/
/*tgpe = (float)4.42410;*/
float gpo = (float)0.0;
float gpe = (float)0.0;
float tgpe = (float)0.0;
float FLOAT_ZERO = 1e-2;
int main(int argc,char **argv)
{
int i;
int j;
int* tree = 0;
int a, b, c;
struct alignment* aln = 0;
struct parameters* param = 0;
struct aln_tree_node* tree2 = 0;
param = malloc(sizeof(struct parameters));
param = interface(param,argc,argv);
// fprintf(stdout,"seq_type=%d\n", param->seq_type); /*debug*/
fprintf(stdout,"custom_sub_matrix_file=%s\n", param->custom_sub_matrix_file); /*debug*/
/*aln = detect_and_read_sequences(aln,param);*/
aln = detect_and_read_sequences_new(aln,param);
#ifdef DEBUG/*{{{*/
/*FILE *fpLog = fopen("logseq.tmp", "w");*/
FILE *fpLog = stderr;
fprintf(fpLog,"\nGap penalties read in\n\n");
for (i = 0 ; i < numseq;i ++){
fprintf(fpLog,">%s\n", aln->sn[i]);
fprintf(fpLog,"%s\n", aln->seq[i]);
if(aln->gpo[i]){
j = 0;
fprintf(fpLog,"%s", "{gpo: ");
for (j = 1;j <= aln->sl[i]; j ++ ) {
fprintf(fpLog,"%g ", aln->gpo[i][j]);
}
fprintf(fpLog,"%s\n", "}");
fprintf(fpLog,"gpo[0]=%g, gpo[%d]=%g\n", aln->gpo[i][0],aln->sl[i]+1, aln->gpo[i][aln->sl[i]+1]);
}
if(aln->gpe[i]){
j = 0;
fprintf(fpLog,"%s", "{gpe: ");
for (j = 1;j <= aln->sl[i]; j ++ ) {
fprintf(fpLog,"%g ", aln->gpe[i][j]);
}
fprintf(fpLog,"%s\n", "}");
fprintf(fpLog,"gpe[0]=%g, gpe[%d]=%g\n", aln->gpe[i][0],aln->sl[i]+1, aln->gpe[i][aln->sl[i]+1]);
}
if(aln->tgpe[i]){
j = 0;
fprintf(fpLog,"%s", "{tgpe: ");
for (j = 1;j <= aln->sl[i]; j ++ ) {
fprintf(fpLog,"%g ", aln->tgpe[i][j]);
}
fprintf(fpLog,"%s\n", "}");
fprintf(fpLog,"tgpe[0]=%g, tgpe[%d]=%g\n", aln->tgpe[i][0],aln->sl[i]+1, aln->tgpe[i][aln->sl[i]+1]);
}
}
if (fpLog != stdout && fpLog != stderr){
fclose(fpLog);
}
fprintf(stderr,"readin sequence output to logseq.tmp\n");
#endif/*}}}*/
if(param->ntree > numseq){
param->ntree = numseq;
}
//DETECT DNA
if(param->dna == -1){
for (i = 0; i < numseq;i++){
param->dna = byg_detect(aln->s[i],aln->sl[i]);
if(param->dna){
break;
}
}
}
//param->dna = 0;
//fprintf(stderr,"DNA:%d\n",param->dna);
//exit(0);
if(param->dna == 1){
//brief sanity check...
for (i = 0; i < numseq;i++){
if(aln->sl[i] < 6){
fprintf(stderr,"Dna/Rna alignments are only supported for sequences longer than 6.");
free(param);
free_aln(aln);
exit(0);
}
}
aln = make_dna(aln);
}
if(param->reformat){
for (i = 0 ;i < numseq;i++){
aln->nsip[i] = i;
for (j = 0; j < aln->sl[i];j++){
aln->s[i][j] = 0;
}
}
param->format = "fasta";//param->reformat;
output(aln,param);
exit(1);
}
//fast distance calculation;
float** submatrix = 0;
// submatrix = read_matrix(submatrix,param); // sets gap penalties as well.....
submatrix = read_matrix_new(submatrix,param); /* modified 2014-11-27 by Nanjiang, accept also customer substitution matrix*/
/*debug print the matrix*/
fprintf(stdout,"\n\n Substitution matrix:\n");
for (i=0;i<23;i++){
for (j=0;j<23;j++){
fprintf(stdout,"%3.0f ", submatrix[i][j]);
}
fprintf(stdout, "\n");
}
fprintf(stdout, "\n\n\n");
if(!param->quiet){
parameter_message(param);
}
if(byg_start(param->alignment_type,"profPROFprofilePROFILE") != -1){
profile_alignment_main(aln,param,submatrix);
}
float** dm = 0;
/*debug*/
/*print para*/
/*debug*/
if(param->ntree > 1)
{
if(byg_start(param->distance,"pairclustalPAIRCLUSTAL") != -1)
{
if(byg_start(param->tree,"njNJ") != -1)
{
dm = protein_pairwise_alignment_distance(aln,dm,param,submatrix,1);
}else
{
dm = protein_pairwise_alignment_distance(aln,dm,param,submatrix,0);
}
}
else if(byg_start("wu",param->alignment_type) != -1)
{
dm = protein_wu_distance2(aln,dm,param);
// param->feature_type = "wumanber";
}
else if(param->dna == 1)
{
if(byg_start(param->tree,"njNJ") != -1)
{
dm = dna_distance(aln,dm,param,1);
}else{
dm = dna_distance(aln,dm,param,0);
}
}else{
if(byg_start(param->tree,"njNJ") != -1)
{
dm = protein_wu_distance(aln,dm,param,1);
}
else
{
dm = protein_wu_distance(aln,dm,param,0); /*this function will be run by default*/
}
}
/*
for (i = 0; i< numseq;i++){
for (j = 0; j< numseq;j++){
fprintf(stderr,"%f ",dm[i][j]);
}
fprintf(stderr,"\n");
}*/
#ifdef DEBUG
/*print the distance matrix*/
fprintf(stderr,"\nThe dm matrix of the size %d x %d:\n",numseq, numseq);
int ii1, jj1;
for (ii1=0;ii1 < numseq; ii1++ ) {
for (jj1=0;jj1 < numseq; jj1++ ) {
fprintf(stderr,"%6g ", dm[ii1][jj1]);
}
fprintf(stderr,"\n");
}
fprintf(stderr,"\n");
#endif
if(byg_start(param->tree,"njNJ") != -1){
tree2 = real_nj(dm,param->ntree);
}else{
tree2 = real_upgma(dm,param->ntree);
}
if(param->print_tree){
print_tree(tree2,aln,param->print_tree);
}
}
tree = malloc(sizeof(int)*(numseq*3+1));
for ( i = 1; i < (numseq*3)+1;i++){
tree[i] = 0;
}
tree[0] = 1;
if(param->ntree < 2){
tree[0] = 0;
tree[1] = 1;
c = numseq;
tree[2] = c;
a = 2;
for ( i = 3; i < (numseq-1)*3;i+=3){
tree[i] = c;
tree[i+1] = a;
c++;
tree[i+2] = c;
a++;
}
}else if(param->ntree > 2){
ntreeify(tree2,param->ntree);
}else{
tree = readtree(tree2,tree);
for (i = 0; i < (numseq*3);i++){
tree[i] = tree[i+1];
}
free(tree2->links);
free(tree2->internal_lables);
free(tree2);
}
/*add to gpo gpe tgpe array*//*{{{*/
for (i = 0 ; i < numseq;i ++){
j=0;
if(!aln->gpo[i]){
aln->gpo[i] = malloc(sizeof(float) * (aln->sl[i]+2));
for (j = 0; j < aln->sl[i]+2; j ++) {
aln->gpo[i][j] = 1.0;
}
} else{
aln->gpo[i][0] = aln->gpo[i][aln->sl[i]+1] = 1.0; /*reset the value of gpo [0] and gpo[length+1] to default, note that when the function detect_and_read_sequences_new is run, gpo, gpe and tgpe haven't been set, fixed 2010-10-29*/
}
if(!aln->gpe[i]){
aln->gpe[i] = malloc(sizeof(float) *(aln->sl[i]+2));
for (j = 0; j < aln->sl[i]+2; j ++) {
aln->gpe[i][j] = 1.0;
}
} else{
aln->gpe[i][0] = aln->gpe[i][aln->sl[i]+1] = 1.0; /*reset the value of gpo [0] and gpo[length+1] to default, note that when the function detect_and_read_sequences_new is run, gpo, gpe and tgpe haven't been set*/
}
if(!aln->tgpe[i]){
aln->tgpe[i] = malloc(sizeof(float) *(aln->sl[i]+2));
for (j = 0; j < aln->sl[i]+2; j ++) {
aln->tgpe[i][j] = 1.0;
}
} else{
aln->tgpe[i][0] = aln->tgpe[i][aln->sl[i]+1] = 1.0; /*reset the value of gpo [0] and gpo[length+1] to default, note that when the function detect_and_read_sequences_new is run, gpo, gpe and tgpe haven't been set*/
}
}/*}}}*/
#ifdef DEBUG/*{{{*/
fpLog = stderr;
fprintf(fpLog,"\nGap penalties after filled in with defaults\n\n");
/*fprintf(fpLog,"\nAfter added gap arrays\n");*/
for (i = 0 ; i < numseq;i ++){
fprintf(fpLog,">%s\n", aln->sn[i]);
fprintf(fpLog,"%s\n", aln->seq[i]);
if(aln->gpo[i]){
j = 0;
fprintf(fpLog,"%s", "{gpo: ");
for (j = 1;j <= aln->sl[i]; j ++ ) {
fprintf(fpLog,"%g ", aln->gpo[i][j]);
}
fprintf(fpLog,"%s\n", "}");
fprintf(fpLog,"gpo[0]=%g, gpo[%d]=%g\n", aln->gpo[i][0],aln->sl[i]+1, aln->gpo[i][aln->sl[i]+1]);
}
if(aln->gpe[i]){
j = 0;
fprintf(fpLog,"%s", "{gpe: ");
for (j = 1;j <= aln->sl[i]; j ++ ) {
fprintf(fpLog,"%g ", aln->gpe[i][j]);
}
fprintf(fpLog,"%s\n", "}");
fprintf(fpLog,"gpe[0]=%g, gpe[%d]=%g\n", aln->gpe[i][0],aln->sl[i]+1, aln->gpe[i][aln->sl[i]+1]);
}
if(aln->tgpe[i]){
j = 0;
fprintf(fpLog,"%s", "{tgpe: ");
for (j = 1;j <= aln->sl[i]; j ++ ) {
fprintf(fpLog,"%g ", aln->tgpe[i][j]);
}
fprintf(fpLog,"%s\n", "}");
fprintf(fpLog,"tgpe[0]=%g, tgpe[%d]=%g\n", aln->tgpe[i][0],aln->sl[i]+1, aln->tgpe[i][aln->sl[i]+1]);
}
}
if (fpLog != stdout && fpLog != stderr){
fclose(fpLog);
}
fprintf(stderr,"readin sequence output to logseq.tmp2\n");
#endif/*}}}*/
for (i = 0 ; i < numseq;i ++){
j=0;
for (j = 0; j < aln->sl[i]+2; j ++) {
aln->gpo[i][j] *= gpo;
aln->gpe[i][j] *= gpe;
aln->tgpe[i][j] *= tgpe;
}
}
#ifdef DEBUG/*{{{*/
fpLog = stderr;
fprintf(fpLog,"\n\n\nGap penalties multipled with gpo (%f), gpe (%f) and tgpe (%f)\n\n", gpo, gpe, tgpe);
/*fprintf(fpLog,"\nAfter added gap arrays\n");*/
for (i = 0 ; i < numseq;i ++){
fprintf(fpLog,">%s\n", aln->sn[i]);
fprintf(fpLog,"%s\n", aln->seq[i]);
if(aln->gpo[i]){
j = 0;
fprintf(fpLog,"%s", "{gpo: ");
for (j = 1;j <= aln->sl[i]; j ++ ) {
fprintf(fpLog,"%g ", aln->gpo[i][j]);
}
fprintf(fpLog,"%s\n", "}");
fprintf(fpLog,"gpo[0]=%g, gpo[%d]=%g\n", aln->gpo[i][0],aln->sl[i]+1, aln->gpo[i][aln->sl[i]+1]);
}
if(aln->gpe[i]){
j = 0;
fprintf(fpLog,"%s", "{gpe: ");
for (j = 1;j <= aln->sl[i]; j ++ ) {
fprintf(fpLog,"%g ", aln->gpe[i][j]);
}
fprintf(fpLog,"%s\n", "}");
fprintf(fpLog,"gpe[0]=%g, gpe[%d]=%g\n", aln->gpe[i][0],aln->sl[i]+1, aln->gpe[i][aln->sl[i]+1]);
}
if(aln->tgpe[i]){
j = 0;
fprintf(fpLog,"%s", "{tgpe: ");
for (j = 1;j <= aln->sl[i]; j ++ ) {
fprintf(fpLog,"%g ", aln->tgpe[i][j]);
}
fprintf(fpLog,"%s\n", "}");
fprintf(fpLog,"tgpe[0]=%g, tgpe[%d]=%g\n", aln->tgpe[i][0],aln->sl[i]+1, aln->tgpe[i][aln->sl[i]+1]);
}
}
if (fpLog != stdout && fpLog != stderr){
fclose(fpLog);
}
fprintf(stderr,"readin sequence output to logseq.tmp2\n");
#endif/*}}}*/
//get matrices...
struct feature_matrix* fm = 0;
struct ntree_data* ntree_data = 0;
int** map = 0;
if(param->ntree > 2){
ntree_data = malloc(sizeof(struct ntree_data));
ntree_data->realtree = tree2;
ntree_data->aln = aln;
ntree_data->profile = 0;
ntree_data->map = 0;
ntree_data->ntree = param->ntree;
ntree_data->submatrix = submatrix;
ntree_data->tree = tree;
ntree_data = ntree_alignment(ntree_data);
map = ntree_data->map;
tree = ntree_data->tree;
for (i = 0; i < (numseq*3);i++){
tree[i] = tree[i+1];
}
free(ntree_data);
}else if (param->feature_type){
fm = get_feature_matrix(fm,aln,param);
if(!fm){
for (i = 32;i--;){
free(submatrix[i]);
}
free(submatrix);
free_param(param);
free(map);
free(tree);
exit(0);
}
map = feature_hirschberg_alignment(aln,tree,submatrix,map,fm);
//exit(0);
//map = feature_alignment(aln,tree,submatrix, map,fm);
}else if (byg_start("pairwise",param->alignment_type) != -1){
if(param->dna == 1){
map = dna_alignment_against_a(aln,tree,submatrix, map,param->gap_inc);
}else{
map = hirschberg_alignment_against_a(aln,tree,submatrix, map,param->smooth_window,param->gap_inc);
}
//map = default_alignment(aln,tree,submatrix, map);
}else if (byg_start("fast",param->alignment_type) != -1){
map = default_alignment(aln,tree,submatrix, map);
}else if(param->dna == 1){
map = dna_alignment(aln,tree,submatrix, map,param->gap_inc);
/*}else if (byg_start("test",param->alignment_type) != -1){
map = test_alignment(aln,tree,submatrix, map,param->internal_gap_weight,param->smooth_window,param->gap_inc);
}else if (param->aa){
map = aa_alignment(aln,tree,submatrix, map,param->aa);
}else if (param->alter_gaps){
map = alter_gaps_alignment(aln,tree,submatrix,map,param->alter_gaps,param->alter_range,param->alter_weight);
}else if (byg_start("altergaps",param->alignment_type) != -1){
map = alter_gaps_alignment(aln,tree,submatrix,map,param->alter_gaps,param->alter_range,param->alter_weight);
}else if(byg_start("simple",param->alignment_type) != -1){
map = simple_hirschberg_alignment(aln,tree,submatrix, map);*/
}else if(byg_start("advanced",param->alignment_type) != -1){
map = advanced_hirschberg_alignment(aln,tree,submatrix, map,param->smooth_window,param->gap_inc,param->internal_gap_weight);
}else{ /*by default, this will be run*/
map = hirschberg_alignment(aln,tree,submatrix, map,param->smooth_window,param->gap_inc);
}
//clear up sequence array to be reused as gap array....
/*After that, aln->s[i][j] will have another meaning
* aln->s[i][j] == 0 means at position j of sequence i, there is no gap,
* aln->s[i][j] == n (n>0) means there are n gaps before position j in sequence i*/
int *p = 0;
for (i = 0; i < numseq;i++){
p = aln->s[i];
for (a = 0; a < aln->sl[i];a++){
p[a] = 0;
}
}
//clear up
for (i = 0; i < (numseq-1)*3;i +=3){
a = tree[i];
b = tree[i+1];
aln = make_seq(aln,a,b,map[tree[i+2]]);
}
#ifdef DEBUG
fprintf(stderr,"\nAfter make_seq\n");
for (i = 0; i < numseq;i++){
fprintf(stderr,"aln->sn[%d]=%s aln->nsip[%d]=%d\n",i, aln->sn[i],i, aln->nsip[i]);
}
#endif
for (i = 0; i < numseq;i++){
aln->nsip[i] = 0;
}
aln = sort_sequences(aln,tree,param->sort);
#ifdef DEBUG
fprintf(stderr,"\nAfter sort_sequences\n");
for (i = 0; i < numseq;i++){
fprintf(stderr,"i=%d aln->nsip[%d]=%d aln->sip[%d][0]=%d\n",i,i, aln->nsip[i],i, aln->sip[i][0]);
}
#endif
#ifdef DEBUG
fprintf(stderr,"\nAligned sequence in digit format\n");
for (i = 0; i < numseq;i++){
fprintf(stderr,">%s\n",aln->sn[aln->nsip[i]]);
j = 0;
for (j = 0; j <= aln->sl[aln->nsip[i]]; j ++){
fprintf(stderr,"%2d ",aln->s[aln->nsip[i]][j]);
}
fprintf(stderr,"\n");
}
#endif
output(aln,param);
/* if(!param->format){
fasta_output(aln,param->outfile);
}else{
if (byg_start("msf",param->format) != -1){
msf_output(aln,param->outfile);
}else if (byg_start("clustal",param->format) != -1){
clustal_output(aln,param->outfile);
}else if (byg_start("macsim",param->format) != -1){
macsim_output(aln,param->outfile,param->infile[0]);
}
}
free_param(param);*/
free(map);
free(tree);
return 0;
}