NAME

GO::AppHandles::AppHandleSqlImpl

SYNOPSIS

you should never use this class directly. Use GO::AppHandle (All the public methods calls are documented there)

DESCRIPTION

implementation of AppHandle for a GO relational database

FEEDBACK

Email cjm@fruitfly.berkeley.edu

get_enriched_term_hash

Args: sample_prods (GP aref) and optional background_prods (GP aref) Returns: enrichment hash array { term=>$term, n_gps_in_sample=>$n_gps_in_sample, n_gps_in_sample_annotated=>$x, gps_in_sample_annotated=>$sample_gps_by_term_id{$term_id}, gps=>$gp_array, n_gps_in_background=>$n_gps_in_background, n_gps_in_background_annotated=>$M, p_value=>$pvalue }

term_anc_bypass

Arg: dbh, list of gp accs, iea usage flag (defaults to 0) Returns: a hashref containing data on the ancestors of terms associated with the gps.

more information by examining the associated SQL

fast_get_enriched_term_hash

Args: sample_prods (GP aref) background_prods (GP aref) (may be optionally empty) speciesdb arrayref iea use flag (defaults to 0) Returns: enrichment hash array { term=>$term, n_gps_in_sample=>$n_gps_in_sample, n_gps_in_sample_annotated=>$k, gps_in_sample_annotated=>$sample_gps_by_term_id{$term_id}, gps=>$gp_array, n_gps_in_background=>$n_gps_in_background, n_gps_in_background_annotated=>$M, p_value=>$pvalue }

NOTE: Experimental version built for speed. WARNING: Check these optimizations against future DB changes.