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authorCalvin Morrison <mutantturkey@gmail.com>2014-03-12 16:06:25 -0400
committerCalvin Morrison <mutantturkey@gmail.com>2014-03-12 16:06:25 -0400
commitfdc2ab95726b27ffabf70a73c00c266aa2717873 (patch)
tree3e84cfc8c79e6232f6f56f7dbe73572517a8ad02 /kmer_counts_per_sequence.c
parent435e6218e8d4faa118cabccdacfeddb589b835ee (diff)
update cli for reverse-compliment counting
Diffstat (limited to 'kmer_counts_per_sequence.c')
-rw-r--r--kmer_counts_per_sequence.c36
1 files changed, 23 insertions, 13 deletions
diff --git a/kmer_counts_per_sequence.c b/kmer_counts_per_sequence.c
index 7e0e119..21aca5a 100644
--- a/kmer_counts_per_sequence.c
+++ b/kmer_counts_per_sequence.c
@@ -12,13 +12,14 @@ void help() {
printf("usage: kmer_counts_per_sequence input_file kmer [kmer-file] ...\n\n"
"count mers in each sequence of size k from a fasta file\n"
"\n"
- " --input -i input fasta file to count\n"
- " --kmer -k size of mers to count\n"
- " --mer-file -m a file containing a list of mers you are interested\n"
- " in opening. this will enable output your results in\n"
- " a sparse format \n"
- " --sparse -s output values in a sparse format. output is in the\n"
- " order sequence_number, mer_index, value\n"
+ " --input -i input fasta file to count\n"
+ " --kmer -k size of mers to count\n"
+ " --compliment -c count compliment of sequences\n"
+ " --mer-file -m a file containing a list of mers you are interested\n"
+ " in opening. this will enable output your results in\n"
+ " a sparse format \n"
+ " --sparse -s output values in a sparse format. output is in the\n"
+ " order sequence_number, mer_index, value\n"
"\n"
"Report all bugs to mutantturkey@gmail.com\n"
"\n"
@@ -55,10 +56,12 @@ int main(int argc, char **argv) {
bool sparse = false;
bool kmer_set = false;
bool specific_mers = false;
+ bool count_compliment = false;
static struct option long_options[] = {
{"input", required_argument, 0, 'i'},
{"kmer", required_argument, 0, 'k'},
+ {"compliment", required_argument, 0, 'c'},
{"sparse", no_argument, 0, 's'},
{"mer-file", required_argument, 0, 'm'},
{"help", no_argument, 0, 'h'},
@@ -70,7 +73,7 @@ int main(int argc, char **argv) {
int option_index = 0;
int c = 0;
- c = getopt_long (argc, argv, "i:k:m:vsh", long_options, &option_index);
+ c = getopt_long (argc, argv, "i:k:m:cvsh", long_options, &option_index);
if (c == -1)
break;
@@ -83,6 +86,8 @@ int main(int argc, char **argv) {
kmer = atoi(optarg);
kmer_set = true;
break;
+ case 'c':
+ count_compliment = true;
case 's':
sparse = true;
break;
@@ -147,7 +152,6 @@ int main(int argc, char **argv) {
unsigned long long sequence = 0;
while ((read = getdelim(&line, &len, '>', fh)) != -1) {
- long long i = 0;
size_t k = 0;
memset(counts, 0, width * sizeof(unsigned long long));
@@ -170,11 +174,17 @@ int main(int argc, char **argv) {
seq[k] = alpha[(int)seq[k]];
}
- for(i = 0; i < (signed long long)(seq_length - kmer + 1); i++) {
- size_t mer = num_to_index(&seq[i],kmer, width, &i);
- counts[mer]++;
+ count_sequence(seq, seq_length, kmer, counts);
+
+ if(count_compliment) {
+ for(k = 0; k < seq_length; k++) {
+ seq[k] = compliment[(int)seq[k]];
+ }
+
+ reverse_string(seq, seq_length);
+ count_sequence(seq, seq_length, kmer, counts);
+
}
-
if(specific_mers) {
for(k = 0; k < num_desired_indicies; k++) {