char * read_line(char sequence[], FILE * pFilePtr)
{
char *pcRes = NULL;
long lineLength = 0;
char current_line_buffer[MAX_READ_BUFFER] = {0};
while((pcRes = fgets(current_line_buffer, sizeof(current_line_buffer), pFilePtr)) != NULL){
if(size_of_string(sequence) > 0)
{
sequence = realloc(sequence, sizeof(char)*(size_of_string(sequence) + size_of_string(current_line_buffer) + 2) );
}
concat_strings_created_with_malloc(sequence,current_line_buffer);
current_line_buffer[0] = '\0';
lineLength = size_of_string(sequence);
//if end of line character is found then exit from loop
if((sequence)[lineLength] == '\n' || (sequence)[lineLength] == '\0'){
break;
}
}
return sequence;
}
void create_phylip_of_snp_sites(char filename[], int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples, int internal_nodes[])
{
FILE *fasta_file_pointer;
int sample_counter;
int snp_counter;
char * base_filename;
base_filename = (char *) calloc(1024,sizeof(char));
memcpy(base_filename, filename, 1024*sizeof(char));
char extension[8] = {".phylip"};
concat_strings_created_with_malloc(base_filename,extension);
fasta_file_pointer = fopen(base_filename, "w");
int number_of_leaves = number_of_samples;
for(sample_counter=0; sample_counter< number_of_samples; sample_counter++)
{
if(internal_nodes[sample_counter] == 1)
{
number_of_leaves--;
}
}
fprintf( fasta_file_pointer, "%d %d\n", number_of_leaves, number_of_snps);
for(sample_counter=0; sample_counter< number_of_samples; sample_counter++)
{
// sequence_name can be more than 10 (relaxed phylip format) and contain [\w\s]
//TODO check for illegal characters [^\w\s]
if(internal_nodes[sample_counter] == 1)
{
continue;
}
fprintf( fasta_file_pointer, "%s\t", sequence_names[sample_counter]);
for(snp_counter=0; snp_counter< number_of_snps; snp_counter++)
{
fprintf( fasta_file_pointer, "%c", bases_for_snps[snp_counter][sample_counter]);
}
fprintf( fasta_file_pointer, "\n");
}
fclose(fasta_file_pointer);
free(base_filename);
}
int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_vcf_file, int output_phylip_file, char output_filename[])
{
size_t length_of_genome;
char * reference_sequence;
int number_of_snps;
int * snp_locations;
int number_of_samples;
int i;
length_of_genome = genome_length(filename);
reference_sequence = (char *) calloc((length_of_genome +1),sizeof(char));
build_reference_sequence(reference_sequence,filename);
number_of_snps = detect_snps(reference_sequence, filename, length_of_genome);
snp_locations = (int *) calloc((number_of_snps+1),sizeof(int));
build_snp_locations(snp_locations, reference_sequence);
free(reference_sequence);
number_of_samples = number_of_sequences_in_file(filename);
// Find out the names of the sequences
char* sequence_names[number_of_samples];
sequence_names[number_of_samples-1] = '\0';
for(i = 0; i < number_of_samples; i++)
{
sequence_names[i] = calloc(MAX_SAMPLE_NAME_SIZE,sizeof(char));
}
get_sample_names_for_header(filename, sequence_names, number_of_samples);
char* bases_for_snps[number_of_snps];
for(i = 0; i < number_of_snps; i++)
{
bases_for_snps[i] = calloc(number_of_samples+1 ,sizeof(char));
}
get_bases_for_each_snp(filename, snp_locations, bases_for_snps, length_of_genome, number_of_snps);
char output_filename_base[MAX_FILENAME_SIZE];
char filename_without_directory[MAX_FILENAME_SIZE];
strip_directory_from_filename(filename, filename_without_directory);
memcpy(output_filename_base,filename_without_directory, size_of_string(filename_without_directory)+1 );
if(output_filename != NULL && *output_filename != '\0')
{
memcpy(output_filename_base,output_filename, size_of_string(output_filename)+1 );
}
if(output_vcf_file)
{
char * vcf_output_filename;
vcf_output_filename = calloc(MAX_FILENAME_SIZE,sizeof(char));
memcpy(vcf_output_filename, output_filename_base, (MAX_FILENAME_SIZE)*sizeof(char));
if((output_vcf_file + output_phylip_file + output_multi_fasta_file) > 1 || (output_filename == NULL || *output_filename == '\0') )
{
char extension[5] = {".vcf"};
concat_strings_created_with_malloc(vcf_output_filename,extension);
}
create_vcf_file(vcf_output_filename, snp_locations, number_of_snps, bases_for_snps, sequence_names, number_of_samples, length_of_genome);
free(vcf_output_filename);
}
if(output_phylip_file)
{
char *phylip_output_filename;
phylip_output_filename = calloc(MAX_FILENAME_SIZE,sizeof(char));
memcpy(phylip_output_filename, output_filename_base, (MAX_FILENAME_SIZE)*sizeof(char));
if((output_vcf_file + output_phylip_file + output_multi_fasta_file) > 1 || (output_filename == NULL || *output_filename == '\0') )
{
char extension[10] = {".phylip"};
concat_strings_created_with_malloc(phylip_output_filename,extension);
}
create_phylib_of_snp_sites(phylip_output_filename, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
free(phylip_output_filename);
}
if((output_multi_fasta_file) || (output_vcf_file ==0 && output_phylip_file == 0 && output_multi_fasta_file == 0))
{
char *multi_fasta_output_filename;
multi_fasta_output_filename = calloc(MAX_FILENAME_SIZE,sizeof(char));
memcpy(multi_fasta_output_filename, output_filename_base, (MAX_FILENAME_SIZE)*sizeof(char));
if((output_vcf_file + output_phylip_file + output_multi_fasta_file) > 1 || (output_filename == NULL || *output_filename == '\0') )
{
char extension[20] = {".snp_sites.aln"};
concat_strings_created_with_malloc(multi_fasta_output_filename,extension);
}
create_fasta_of_snp_sites(multi_fasta_output_filename, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
free(multi_fasta_output_filename);
}
// free memory
free(snp_locations);
for(i = 0; i < number_of_samples; i++)
{
free(sequence_names[i]);
}
for(i = 0; i < number_of_snps; i++)
{
free(bases_for_snps[i]);
}
return 1;
}
