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kalignP_interface.c
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kalignP_interface.c
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/*
kalignP_interface.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 <string.h>
#include <getopt.h>
//#include <unistd.h>
#include "kalignP.h"
#include "kalignP_input.h"
void parameter_message(struct parameters* param)
{
if(param->infile[0]){
if(param->dna){
fprintf(stderr,"Aligning %d RNA/DNA sequences from file %s with these parameters:\n",numseq,param->infile[0]);
}else{
fprintf(stderr,"Aligning %d protein sequences from file %s with these parameters:\n",numseq,param->infile[0]);
}
}else{
if(param->dna){
fprintf(stderr,"Aligning %d RNA/DNA sequences with these parameters:\n",numseq);
}else{
fprintf(stderr,"Aligning %d protein sequences with these parameters:\n",numseq);
}
}
// fprintf(stderr," Distance estimation method: %s\n",param->distance);
//fprintf(stderr," Tree building method: %s\n",param->tree);
//fprintf(stderr," Ntree: %d\n",param->ntree);
//fprintf(stderr," %0.8f gap open penalty\n",(float)gpo/5);
fprintf(stderr," %0.8f gap open penalty\n",(float)gpo);
//fprintf(stderr," %0.8f gap extension\n",(float)gpe/10);
fprintf(stderr," %0.8f gap extension\n",(float)gpe);
//fprintf(stderr," %0.8f terminal gap penalty\n",(float)tgpe/10);
fprintf(stderr," %0.8f terminal gap penalty\n",(float)tgpe);
//fprintf(stderr," %0.8f bonus\n",param->secret/10);
fprintf(stderr," %0.8f bonus\n",param->secret);
/*fprintf(stderr," %0.2f zlevel\n",param->zlevel);
fprintf(stderr," %0.2f igw\n",param->internal_gap_weight);
fprintf(stderr," %d sw\n",param->smooth_window);
fprintf(stderr," %0.2f smo\n", param->gap_inc);*/
if(param->outfile){
fprintf(stderr,"Alignment will be written to file:'%s'.\n\n",param->outfile);
}else{
fprintf(stderr,"Alignment will be written to stdout.\n\n");
}
}
struct parameters* interface(struct parameters* param,int argc,char **argv)
{
int i,c;
param->gpo = -1.0;
param->gpe = -1.0;
param->tgpe = -1.0;
param->secret = -1.0;
param->zlevel = 58.8;
param->sub_matrix = 0;
param->aa = 0;
param->infile = malloc(sizeof(char*)*3);
param->infile[0] = 0;
param->infile[1] = 0;
param->infile[2] = 0;
param->input = 0;
param->outfile = 0;
param->format = 0;
param->help_flag = 0;
param->quiet = 0;
param->id = -1;
param->distance = "wu";
param->reformat = 0;
param->sort = 0;
param->print_svg_tree = 0;
param->dna = -1;
param->feature_type = 0;
param->alignment_type = "default";
param->tree = "upgma";
param->ntree = 2;
param->print_tree = 0;
param->alter_gaps = 0;
param->alter_range = 0.5;
param->alter_weight = 100;
param->internal_gap_weight = 0;
param->smooth_window = 1;
param->gap_inc = 0.0;
param->same_feature_score = 75;
param->diff_feature_score = -5;
param->custom_sub_matrix_file = 0; /*added 2014-11-27 by Nanjiang, customer substitution matrix file*/
param->seq_type = -1; /*added 2014-11-27 by Nanjiang, by default, do not set any seq_type, 0: protein, 1: dna, 2: rna*/
/*static char license[] = "\n\*/
/*Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann\n\n\*/
/*Kalign is free software. You can redistribute it and/or modify\n\*/
/*it under the terms of the GNU General Public License as\n\*/
/*published by the Free Software Foundation.\n\n";*/
static char license[] = "\n\
KalignP version 1.0, Copyright (C) 2010 Nanjiang Shu\n\n\
Multiple sequence alignment with position specific gap penalties\n\n\
KalignP is derived from Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann\n\n\
KalignP is free software. You can redistribute it and/or modify\n\
it under the terms of the GNU General Public License as\n\
published by the Free Software Foundation.\n\n";
while (1){
static struct option long_options[] ={
{"gapopen", required_argument, 0,'s'}, /*0*/
{"gpo", required_argument, 0, 's'}, /*1*/
{"gapextension", required_argument, 0, 'e'}, /*2*/
{"gpe", required_argument, 0, 'e'}, /*3*/
{"secret", required_argument, 0, 'm'}, /*4*/
{"bonus", required_argument, 0, 'm'}, /*5*/
{"terminalgapextension", required_argument, 0, 't'}, /*6*/
{"tgpe", required_argument, 0, 't'}, /*7*/
{"zcutoff", required_argument, 0, 0}, /*8*/
{"distance", required_argument, 0, 'd'}, /*9*/
{"ntree", required_argument, 0, 0}, /*10*/
{"tree", required_argument, 0, 0}, /*11*/
{"format", required_argument, 0, 'f'}, /*12*/
{"reformat", 0, 0, 'r'}, /*13*/
{"sort",required_argument,0,'c'}, /*14*/
{"feature", required_argument, 0, 0}, /*15*/
{"type", required_argument, 0, 0}, /*16*/
{"alter_gaps", required_argument, 0, 0}, /*17*/
{"altergaps", required_argument, 0, 0}, /*18*/
{"alter_range", required_argument, 0, 0}, /*19*/
{"alter_weight", required_argument, 0, 0}, /*20*/
{"internal_gap_weight", required_argument, 0, 0}, /*21*/
{"smooth_window", required_argument, 0, 0}, /*22*/
{"gap_inc", required_argument, 0, 'a'}, /*23*/
{"matrix", required_argument, 0, 0}, /*24*/
{"mmbonus", required_argument, 0, 0}, /*25*/
{"nuc", 0, 0, 0}, /*26*/
{"dna", 0, 0, 0}, /*27*/
{"rna", 0, 0, 0}, /*28*/
{"protein", 0, 0, 0}, /*29*/
{"profile", 0, 0, 0}, /*30*/
{"prof", 0, 0, 0}, /*31*/
{"id", required_argument, 0, 0}, /*32*/
{"printtree", required_argument, 0, 0}, /*33*/
{"svgtree", required_argument, 0, 0}, /*34*/
{"svg_tree", required_argument, 0, 0}, /*35*/
{"pairwise", 0, 0, 0}, /*36*/
{"same_feature_score", required_argument, 0, 0}, /*37*/
{"diff_feature_score", required_argument, 0, 0}, /*38*/
{"custom_matrix", required_argument, 0, 0}, /*39*/
{"seq_type", required_argument, 0, 0}, /*40*/
{"input", required_argument, 0, 'i'}, /*41*/
{"infile", required_argument, 0, 'i'}, /*42*/
{"in", required_argument, 0, 'i'}, /*43*/
{"output", required_argument, 0, 'o'}, /*44*/
{"outfile", required_argument, 0, 'o'}, /*45*/
{"out", required_argument, 0, 'o'}, /*46*/
{"help", no_argument,0,'h'}, /*47*/
{"quiet", 0, 0, 'q'}, /*48*/
{0, 0, 0, 0} /*49*/
};
int option_index = 0;
c = getopt_long_only (argc, argv,"i:o:hqs:e:m:t:z:c:f:d:b:a:r",long_options, &option_index);
//c = getopt (argc, argv, "hi:o:");
/* Detect the end of the options. */
if (c == -1){
break;
}
switch (c){
case 0:
if (long_options[option_index].flag != 0){
break;
}
switch (option_index){
case 0:
case 1:
fprintf(stderr,"GAGAGA\n");
param->gpo = atof(optarg);
break;
case 2:
case 3:
param->gpe = atof(optarg);
break;
case 4:
case 5:
param->secret = atof(optarg);
break;
case 6:
case 7:
param->tgpe = atof(optarg);
break;
case 8:
param->zlevel = atof(optarg);
break;
case 9:
param->distance = optarg;
break;
case 10:
param->ntree = atoi(optarg);
break;
case 11:
param->tree = optarg;
break;
case 12:
param->format = optarg;
break;
case 13:
param->reformat = 1;
break;
case 14:
param->sort = optarg;
break;
case 15:
param->feature_type = optarg;
break;
case 16:
param->alignment_type = optarg;
break;
case 17:
case 18:
param->alter_gaps = atoi(optarg);
break;
case 19:
param->alter_range = atof(optarg);
break;
case 20:
param->alter_weight = atoi(optarg);
break;
case 21:
param->internal_gap_weight = atof(optarg);
break;
case 22:
param->smooth_window = atoi(optarg);
break;
case 23:
param->gap_inc = atof(optarg);
break;
case 24:
param->sub_matrix = optarg;
break;
case 25:
param->aa = atoi(optarg);
break;
case 26:
case 27:
case 28:
param->dna = 1;
break;
case 29:
param->dna = 0;
break;
case 30:
case 31:
param->alignment_type = "profile";
break;
case 32:
param->id = atoi(optarg);
break;
case 33:
param->print_tree = optarg;
break;
case 34:
case 35:
param->print_svg_tree = optarg;
break;
case 36:
param->alignment_type = "pairwise";
break;
case 37:
param->same_feature_score = atof(optarg);//"pairwise";
break;
case 38:
param->diff_feature_score = atof(optarg);//lignment_type = "pairwise";
break;
case 39:
param->custom_sub_matrix_file = optarg;/*customer substitution matrix file*/
break;
case 40:
param->seq_type = atoi(optarg);/*seq_type, 0: protein, 1: dna, 2: rna*/
break;
default:
break;
}
//printf ("option%d %s",option_index,long_options[option_index].name);
//if (optarg){
// printf (" with arg %s\n", optarg);
//}
break;
case 's':
param->gpo = atof(optarg);
//param->help_flag = 1;
break;
case 'e':
param->gpe = atof(optarg);
break;
case 'm':
param->secret = atof(optarg);
break;
case 't':
param->tgpe = atof(optarg);
break;
case 'z':
param->zlevel = atof(optarg);
break;
case 'c':
param->sort = optarg;
break;
case 'f':
param->format = optarg;
break;
case 'r':
param->reformat = 1;
break;
case 'd':
param->distance = optarg;
break;
case 'b':
param->tree = optarg;
break;
case 'h':
param->help_flag = 1;
break;
case 'i':
param->infile[1] = optarg;
break;
case 'o':
param->outfile = optarg;
break;
case 'a':
param->gap_inc = atof(optarg);
break;
case 'q':
param->quiet = 1;
break;
case '?':
free_param(param);
exit(1);
break;
default:
abort ();
}
}
if (optind < argc){
c = 0;
if(param->infile[1]){
i = 3;
}else{
i = 2;
}
/*fprintf(stderr,"EXTRA :%d\n",argc - optind); */
param->infile = realloc(param->infile,(sizeof(char*) * (argc - optind+i)));
for (c = i-1 ; c < (argc - optind+i);c++){
param->infile[c] = 0;
}
c = i-1;
while (optind < argc){
/*switch(c){
case 0:
param->infile[c] = argv[optind++];
break;
case 1:
param->outfile = argv[optind++];
break;
default:
fprintf(stderr,"Unrecognised junk:%s\n",argv[optind++]);
break;
}*/
param->infile[c] = argv[optind++];
c++;
}
}
//exit(0);
if (byg_start("pairwise",param->alignment_type) != -1){
param->ntree = 1;
if(param->tgpe == -1.0){
param->tgpe = 0.0f;
}
}
if(param->gap_inc < 0.0){
fprintf(stderr,"%s\n", usage);
fprintf(stderr,"Invalid parameter setting: gap_inc needs to be > 0 \n");
exit(1);
}
if(param->quiet){
fclose(stderr);
}
fprintf(stderr,"%s", license);
if (param->help_flag){
fprintf(stderr,"%s\n", usage);
exit(1);
}
//exit(0);
/*if (!param->infile[1]){
fprintf(stderr,"%s\n", usage);
exit(1);
}*/
return param;
}