Provided by: phast_1.5+dfsg-1_amd64
eval_predictions - Compares predicted genes with "real" (or annotated) genes.
eval_predictions -r <real_fname_list> -p <pred_fname_list> -l <seq_len_list> [OPTIONS]
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').
-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.