load-files.scm

;
; load-files.scm
;
; Quick-n-dirty hacky wrapper to load the genome/proteome datasets
; into the AtomSpace. A required first step for performing network
; analysis.
;
; Usage:
; guile> (load "load-files.scm")
; guile> (load-all)
;
(use-modules (opencog))
(use-modules (opencog persist))
(use-modules (opencog persist-file))
(use-modules (opencog bioscience))
(use-modules (opencog cogserver))

(define (loaf fn)
	(define start (current-time))
	(define ssz (count-all))
	(define path (string-append "/home/ubuntu/datasets/" fn))
	;
	; load-file is from (opencog persist-file)
	; and it is about 8x faster than `primitive-load`
	; (define jnk (primitive-load path))
	(define jnk (load-file path))
	(define delapse (- (current-time) start))
	(define elapse (if (eq? delapse 0) 1 delapse))
	(define delta (- (count-all) ssz))
	(define rate (/ (exact->inexact delta) elapse))
	(format #t "Took ~A secs to load ~A\n" elapse fn)
	(format #t "Loaded ~A atoms (~A per sec) total atoms=~A\n"
		delta rate (count-all))
	; (format #t "Atomspace = ~A\n" (cog-report-counts))
	*unspecified*
)

(define file-list (list
 "biogridgene2uniprot.scm"
 "biogrid_gene_gene_174.scm"
 "ChEBI2Reactome_PE_Pathway.txt.scm"
 "current_symbols.scm"
 "entrez_to_protein.scm"
 "GO_annotation.scm"
 "GO_without_def.scm"
 "NCBI2Reactome_PE_Pathway.txt.scm"
 "reactome.scm"
 "smpdb_chebi_wname.scm"
 "smpdb_protein.scm"
 "uniprot2GO.scm"
 "UniProt2Reactome_PE_Pathway.txt.scm"
))

(define current-2019-list (list
 "current-2019-12-31/biogridgene2uniprot.scm"
 "current-2019-12-31/biogrid_gene_gene_3.5.177.scm"
 "current-2019-12-31/ChEBI2Reactome_PE_Pathway.txt.scm"
 "current-2019-12-31/entrez_to_protein.scm"
 "current-2019-12-31/GO.scm"
 "current-2019-12-31/GO_annotation.scm"
 "current-2019-12-31/NCBI2Reactome_PE_Pathway.txt.scm"
 "current-2019-12-31/reactome.scm"
 "current-2019-12-31/uniprot2GO.scm"
 "current-2019-12-31/UniProt2Reactome_PE_Pathway.txt.scm"
))

(define current-list (list
	"current/ChEBI2Reactome_PE_Pathway.txt.scm"
	"current/biogrid_gene_gene_3.5.177.scm"
	"current/noncodingRNA.scm"
	"current/smpdb_protein.scm"
	"current/NCBI2Reactome_PE_Pathway.txt.scm"
	"current/uniprot2GO.scm"
	"current/UniProt2Reactome_PE_Pathway.txt.scm"
	"current/reactome.scm"
	"current/GO_annotation.scm"
	"current/entrez_to_protein.scm"
	"current/current_symbols.scm"
	"current/smpdb_chebi_wname.scm"
	"current/biogridgene2uniprot.scm"
	"current/codingRNA.scm"
	"current/GO.scm"
))

(define (load-all)
	(define start (current-time))
	(for-each loaf current-list)
	(format #t "\nLoaded all the files in ~A seconds\n" (- (current-time) start))
	#f
)

; (start-cogserver)
; (start-cogserver "path.conf")
; (start-cogserver "grid.conf")
(display "Don't forget to (start-cogserver \"path.conf\")\n")
(display "   or to (start-cogserver \"grid.conf\")\n")

*unspecified*