https://github.com/sanger-pathogens/gubbins
Tip revision: 0dfe1234ef48c2808e9b80809ea962e87ec2054a authored by Nick Croucher on 31 October 2022, 05:28:42 UTC
Merge and improve clade analysis scripts
Merge and improve clade analysis scripts
Tip revision: 0dfe123
gff_file.c
/*
* Wellcome Trust Sanger Institute
* Copyright (C) 2011 Wellcome Trust Sanger Institute
*
* 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 (at your option) 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., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "gff_file.h"
void print_gff_header(FILE * gff_file_pointer, int genome_length)
{
fprintf(gff_file_pointer, "##gff-version 3\n");
fprintf(gff_file_pointer, "##sequence-region SEQUENCE 1 %d\n", genome_length);
fflush(gff_file_pointer);
}
void print_gff_line(FILE * gff_file_pointer, int start_coordinate, int end_coordinate, int number_of_snps, char * current_node_id, char * parent_node_id, char * taxon_names, double neg_log_likelihood)
{
fprintf(gff_file_pointer, "SEQUENCE\tGUBBINS\tCDS\t");
fprintf(gff_file_pointer, "%d\t",start_coordinate);
fprintf(gff_file_pointer, "%d\t",end_coordinate);
fprintf(gff_file_pointer, "0.000\t.\t0\t");
fprintf(gff_file_pointer, "node=\"%s->%s\";", parent_node_id, current_node_id );
fprintf(gff_file_pointer, "neg_log_likelihood=\"%f\";", neg_log_likelihood);
fprintf(gff_file_pointer, "taxa=\"%s\";", taxon_names);
fprintf(gff_file_pointer, "snp_count=\"%d\";", number_of_snps);
fprintf(gff_file_pointer, "\n");
fflush(gff_file_pointer);
}