read_selection.c

/*
# This source code is part of icgc, an ICGC processing pipeline.
#
# Icgc 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 3 of the License, or
# (at your option) any later version.
#
# Icgc 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, see<http://www.gnu.org/licenses/>.
#
# Contact: ivana.mihalek@gmail.com
#
#
# Original publication:  https://www.ncbi.nlm.nih.gov/pubmed/12875851
#
#
*/

# include <stdio.h>
# include <stdlib.h>
# include <math.h>
# include <string.h>
# include "utils.h"
# include "pdbclust.h"
/*
   input format
   F  3
   K  48
   R  50
   D  59
   C  62
   G  71
   A  78
   Y  79
   E  82
   G  91
   A  97
   C  100
   G  102
   L  109
   etc
 */


/****************************************************************************/
int errmsg ( FILE *fptr, int line_ctr, char line[LONGSTRING],
													char * fmt, char * warnstr) {

			fprintf ( fptr, "Error on line %3d:     %s", line_ctr, line);
			fprintf ( fptr, fmt, warnstr);
			return 0;
}
/****************************************************************************/
int read_selection (Residue *sequence, int no_res, char * filename, int * selection) {
			FILE * fptr, *log = stdout;
			char line[LONGSTRING];
			char token[MAX_TOK][MEDSTRING] = {{'\0'}};
			char comment_char;
			int line_ctr = 0, retval;
			int max_token;
			/***************/

			int i;
			char res_short;

			fptr   = efopen ( filename, "r" );
			if (!fptr ) return 1;
			memset ( line, 0, LONGSTRING);
			while(fgets(line,LONGSTRING,fptr)!=NULL) {
											line_ctr++;
											/* tokenize */
											retval = tokenize ( token, &max_token, line, comment_char= '!' );
											switch ( retval ) {
											case  TOK_TOOMNY:
																			errmsg ( log, line_ctr, line, "\t\t %s\n", "Too many tokens.");
																			fclose (log);
																			break;
											case TOK_TOOLONG:
																			errmsg ( log, line_ctr, line, "\t\t %s\n", "Token too long.");
																			fclose (log);
																			break;
											}
											if ( max_token < 0 ) continue;
											res_short = token[0][0];
											for (i=0; i<no_res; i++) {
																			if (!strcmp(sequence[i].pdb_id, token[1]) ) {
																											/* check */
																											if ( res_short != sequence[i].res_type_short) {
																																			fprintf (stderr, "type mismatch: %s  %c  %c \n",
																																												sequence[i].pdb_id, res_short, sequence[i].res_type_short);
																																			exit(1);
																											}
																											selection[i] = 1;
																											break;
																			}
											}
			}
			int no_selected = 0;
			for (i=0; i<no_res; i++) no_selected += selection[i];
			printf ("selected: %d\n", no_selected);

			return 0;
}