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Change location of where ListLink wrapping occurs. #165

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Change location of where ListLink wrapping occurs. #165

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27 changes: 14 additions & 13 deletions annotation/functions.scm
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Original file line number Diff line number Diff line change
Expand Up @@ -436,8 +436,9 @@ in the specified namespaces."
If do-protein is #t then protein interactions are included.
"
(map
(lambda (act-gene)
(generate-result gene act-gene do-protein namespace parents coding non-coding))
(lambda (act-gene) (ListLink
(generate-result gene act-gene do-protein
namespace parents coding non-coding)))

(run-query (Get
(VariableList
Expand All @@ -459,8 +460,8 @@ in the specified namespaces."
If do-protein is #t then protein interactions are included.
"
(map
(lambda (gene-pair)
(generate-result (gar gene-pair) (gdr gene-pair) do-protein namespace parents coding non-coding))
(lambda (gene-pair) (ListLink
(generate-result (gar gene-pair) (gdr gene-pair) do-protein namespace parents coding non-coding)))

(run-query (Get
(VariableList
Expand Down Expand Up @@ -544,7 +545,7 @@ in the specified namespaces."

;; ---------------------------------

(define-public (generate-result gene-a gene-b do-protein namespaces num-parents
(define (generate-result gene-a gene-b do-protein namespaces num-parents
coding-rna non-coding-rna)
"
generate-result -- add info about matched variable nodes
Expand All @@ -562,7 +563,7 @@ in the specified namespaces."
(if
(or (equal? (cog-type gene-a) 'VariableNode)
(equal? (cog-type gene-b) 'VariableNode))
(ListLink)
'()
(let* (
[already-done-a ((biogrid-genes) gene-a)]
[already-done-b ((biogrid-genes) gene-b)]
Expand Down Expand Up @@ -604,8 +605,8 @@ in the specified namespaces."
[coding-prot-b (find-protein-form gene-b)])
(if (or (equal? coding-prot-a (ListLink))
(equal? coding-prot-b (ListLink)))
(ListLink)
(ListLink
'()
(list
interaction
(Evaluation (Predicate "expresses") (List gene-a coding-prot-a))
(node-info gene-a)
Expand All @@ -619,7 +620,7 @@ in the specified namespaces."
rna-cross-annotation
)
))
(ListLink
(list
interaction
(node-info gene-a)
(locate-node gene-a)
Expand Down Expand Up @@ -652,8 +653,8 @@ in the specified namespaces."
(if do-protein
(let ([coding-prot (find-protein-form gene-x)])
(if (equal? coding-prot (ListLink))
(ListLink)
(ListLink
'()
(list
interaction
(Evaluation (Predicate "expresses") (List gene-x coding-prot))
(node-info gene-x)
Expand All @@ -662,7 +663,7 @@ in the specified namespaces."
go-cross-annotation
rna-cross-annotation)
))
(ListLink
(list
interaction
(node-info gene-x)
(locate-node gene-x)
Expand All @@ -671,7 +672,7 @@ in the specified namespaces."
)))

;;; Both of the genes have been done.
(else (if already-done-pair (ListLink) (ListLink interaction)))
(else (if already-done-pair '() (list interaction)))
)
)
)
Expand Down