PROGRAM: eval_predications

USAGE: eval_predictions -r <real_fname_list> -p <pred_fname_list>
                        -l <seq_len_list> [OPTIONS] 

DESCRIPTION:
Compares predicted genes with "real" (or annotated) genes.
Reports standard measures of prediction quality.  The following
measures are reported:

    - nucleotide sensitivity (Sn)
    - nucleotide specificity (Sp)
    - approximate correlation (AC)
    - correlation coefficient (CC)
    - exon sensitivity (ESn)
    - exon specificity (ESp)
    - proportion of real exons correctly predicted (CRa)
    - proportion of real exons partially predicted (PCa)
    - proportion of real exons with overlapping predictions (OLa)
    - missed exons (ME)
    - proportion of predicted exons that are correct (CRp)
    - proportion of predicted exons that are partially correct (PCp)
    - proportion of predicted exons that overlap real ones (OLp)
    - wrong exons (WE)

All quantities are computed as described in "Evaluation of Gene-Finding
Programs on Mammalian Sequences," by Rogic et al. (Genome Research
11:817-832).  Note that CRa + PCa + OLa + ME = 1 and CRp + PCp + OLp +
WE = 1.  Note also that each set (predicted and real) should consist of
non-overlapping groups of features (see 'refeature').

OPTIONS:
    -r <real_fname_list> 
        (required) List of names of files defining real genes (GFF). 

    -p <pred_fname_list> 
        (required) List of names of files defining predicted genes
        (GFF).  Must correspond in order to <real_fname_list>.

    -l <seq_len_list>
        (required) List of lengths of sequences.  Needed to compute
        certain nucleotide-level statistics.

    -f <feat_list>  
        List of names of all features denoting exon regions.  By
        default, equal to the single name "CDS".

    -d <fname_prefix>  
        Dump full coords of correct, partially correct, wrong, missed, 
        and overlapping exons to a set of files having the specified 
        file name prefix.

    -n <nbases>
        Also report stats on "nearly correct" exons, that is, incorrect
        exons whose boundaries are within <nbases> of being correct.
        Columns will be labeled "NCa" and "NCp".

    -h
        Print this help message.


NOTE: be sure stop codons are included in CDSs in both the predicted
and real sets, or in neither set.