libuproc  1.2.0
Modules | Macros | Typedefs | Functions

  
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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...
 

Detailed Description

 

Macro Definition Documentation

#define UPROC_ORF_FRAMES   6

Number of possible frames (forward and reverse)

Typedef Documentation

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.

Function Documentation

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.)

Parameters
scoresOUT: scores for all possible binary codons (must be a pointer into an array of at least UPROC_BINARY_CODON_COUNT elements)
score_matrixcodon scores, size UPROC_CODON_COUNT x 1