analyse_networks.af

# @author Pedro Seoane Zonjic, Fernando Moreno Jabato

split_hpo_for_analysis){
	cut -f 1 $working_net |sort -u > uniq_hpo
	?
	split -d -n l/$n_frags uniq_hpo frag_
}

term_pairs_enrichment_analysis){
	resources: -n cal -c 2 
	echo [cpu]
	source ~soft_bio_267/initializes/init_R
	net_name=`basename $working_net`
	type_terms=`echo $clprof_enrichments | tr ':' ' '`
	type_terms_array=( $type_terms )
	for term in ${type_terms_array[@]}
	do
	    ?
	    enrich_by_onto.R -p $pval_thresold -e $term -o $term'_enrichment' -n $working_net -t $net_name -f&
	done
	wait
}

enrichment_analysis_[BP;MF;%CC]){
	resources: -n cal -c $n_frags
	echo [cpu]
	source ~soft_bio_267/initializes/init_R
	net_name=`basename $working_net`
	for i in {1..$n_frags}
	do
		count=$(( i - 1 ))
		grep -F -f 'split_hpo_for_analysis)/frag_0'$count $working_net > 'sample_'$i
		rm 'enrichment_table_'$i
		?
		topgo_enrich.R -d 'sample_'$i -o 'enrichment_table_'$i -p $pval_thresold -s (*) -t $net_name&
	done
	wait
		# lines=`wc -l < enrichment_table`
		# if (( $lines =< 1 )) ; exit 1 ; fi
}