libuproc
1.2.0
|
Modules | |
struct uproc_orf | |
Open reading frame. | |
object uproc_orfiter | |
Iterates over a DNA/RNA sequence and yield all possible ORFs. | |
Macros | |
#define | UPROC_ORF_FRAMES 6 |
Number of possible frames (forward and reverse) More... | |
Typedefs | |
typedef bool | uproc_orffilter(const struct uproc_orf *, const char *, size_t, double, void *) |
ORF filter function. More... | |
Functions | |
void | uproc_orf_codonscores (double *scores, const uproc_matrix *score_matrix) |
Prepare codon score table. More... | |
#define UPROC_ORF_FRAMES 6 |
Number of possible frames (forward and reverse)
typedef bool uproc_orffilter(const struct uproc_orf *, const char *, size_t, double, void *) |
ORF filter function.
The function should take an ORF, the DNA sequence, it's length and GC content and finally a user-supplied "opaque" pointer as arguments and return whether the ORF is accepted or not.
void uproc_orf_codonscores | ( | double * | scores, |
const uproc_matrix * | score_matrix | ||
) |
Prepare codon score table.
Turns a uproc_matrix of size UPROC_CODON_COUNT x 1
into a double array suitable for uproc_orfiter_create(). The score of a codon containing wildcards is the mean value of all codons that match it. Stop codons don't get a score (it is ignored anyway)
If score_matrix
is NULL, all entries of scores
are set to 0.
(This is a quite costly operation, so doing this once instead of every time a uproc_orfiter is created can save a lot of time.)
scores | OUT: scores for all possible binary codons (must be a pointer into an array of at least UPROC_BINARY_CODON_COUNT elements) |
score_matrix | codon scores, size UPROC_CODON_COUNT x 1 |