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Choose output file formats #2

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Jan 25, 2012
Merged

Choose output file formats #2

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55 changes: 39 additions & 16 deletions main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -20,36 +20,59 @@
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <unistd.h>
#include "snp_sites.h"

#define MAX_FILENAME_SIZE 250

static void print_usage()
{
printf("Find SNP sites from a multi fasta alignment file (which can be gzipped)\n");
printf("./snp_sites file.aln\n");
printf("./snp_sites file.aln.gz\n\n");

printf("SNP sites are outputted in the following formats: Multi fasta alignment, phylip, VCF \n\n");
printf("Usage: snp_sites [-mvph] <file>\n");
printf("This program finds snp sites from a multi fasta alignment file.\n");
printf(" -m output a multi fasta alignment file (default)\n");
printf(" -v output a VCF file\n");
printf(" -p output a phylip file\n");
printf(" -h this help message\n");
printf(" <file> input alignment file which can optionally be gzipped\n");
}

int main (int argc, const char * argv[]) {
int main (int argc, char **argv) {
char multi_fasta_filename[MAX_FILENAME_SIZE];

if(argc <=1)
{
print_usage();
}
else if(strcmp(argv[1], "--help") == 0)
int c;
int index;
int output_multi_fasta_file = 0;
int output_vcf_file = 0;
int output_phylip_file = 0;

while ((c = getopt (argc, argv, "mvp:")) != -1)
switch (c)
{
case 'm':
output_multi_fasta_file = 1;
break;
case 'v':
output_vcf_file = 1;
break;
case 'p':
output_phylip_file = 1;
break;
case 'h':
print_usage();
return 0;
default:
output_multi_fasta_file = 1;
}

if(optind < argc)
{
print_usage();
strcpy(multi_fasta_filename,argv[optind]);
generate_snp_sites(multi_fasta_filename, output_multi_fasta_file, output_vcf_file, output_phylip_file);
}
else
{
strcpy(multi_fasta_filename,argv[1]);
generate_snp_sites(multi_fasta_filename);
print_usage();
}


return 0;
}
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3 changes: 3 additions & 0 deletions makefile
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Expand Up @@ -25,3 +25,6 @@ vcf.o: vcf.c
clean:
-rm *.o

test:
cd tests && make

Binary file modified snp_sites
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18 changes: 15 additions & 3 deletions snp_sites.c
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Expand Up @@ -45,7 +45,7 @@ void build_snp_locations(int snp_locations[], char reference_sequence[])
}


int generate_snp_sites(char filename[])
int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_vcf_file, int output_phylip_file)
{
int length_of_genome;
char * reference_sequence;
Expand Down Expand Up @@ -87,10 +87,22 @@ int generate_snp_sites(char filename[])

char filename_without_directory[MAX_FILENAME_SIZE];
strip_directory_from_filename(filename, filename_without_directory);


create_vcf_file(filename_without_directory, snp_locations, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
if(output_vcf_file)
{
create_vcf_file(filename_without_directory, snp_locations, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
}

if(output_phylip_file)
{
create_phylib_of_snp_sites(filename_without_directory, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
create_fasta_of_snp_sites(filename_without_directory, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
}

if((output_multi_fasta_file) || (output_vcf_file ==0 && output_phylip_file == 0 && output_multi_fasta_file == 0))
{
create_fasta_of_snp_sites(filename_without_directory, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
}

free(snp_locations);
return 1;
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2 changes: 1 addition & 1 deletion snp_sites.h
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Expand Up @@ -21,7 +21,7 @@
#define _SNP_SITES_H_

void build_snp_locations(int snp_locations[], char reference_sequence[]);
int generate_snp_sites(char filename[]);
int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_vcf_file, int output_phylip_file);
int refilter_existing_snps(char * reference_bases, int number_of_snps, char ** column_names, int number_of_columns,int * snp_locations, int * filtered_snp_locations);
void remove_filtered_snp_locations(int * filtered_snp_locations, int * snp_locations, int number_of_snps);
void strip_directory_from_filename(char * input_filename, char * output_filename);
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6 changes: 3 additions & 3 deletions tests/check_snp_sites.c
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Expand Up @@ -9,7 +9,7 @@

START_TEST (valid_alignment_with_one_line_per_sequence)
{
generate_snp_sites("data/alignment_file_one_line_per_sequence.aln");
generate_snp_sites("data/alignment_file_one_line_per_sequence.aln",1,1,1);
fail_unless( compare_files("data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" );
fail_unless( compare_files("data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" );
fail_unless( compare_files("data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq");
Expand All @@ -22,7 +22,7 @@ END_TEST

START_TEST (valid_alignment_with_one_line_per_sequence_gzipped)
{
generate_snp_sites("data/alignment_file_one_line_per_sequence.aln.gz");
generate_snp_sites("data/alignment_file_one_line_per_sequence.aln.gz",1,1,1);
fail_unless( compare_files("data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.gz.vcf" ) == 1, "Invalid VCF file for 1 line per seq" );
fail_unless( compare_files("data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.gz.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" );
fail_unless( compare_files("data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.gz.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq");
Expand All @@ -34,7 +34,7 @@ END_TEST

START_TEST (valid_alignment_with_multiple_lines_per_sequence)
{
generate_snp_sites("data/alignment_file_multiple_lines_per_sequence.aln");
generate_snp_sites("data/alignment_file_multiple_lines_per_sequence.aln",1,1,1);
fail_unless( compare_files("data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_multiple_lines_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" );
fail_unless( compare_files("data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_multiple_lines_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" );
fail_unless( compare_files("data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq");
Expand Down