From 7dc82124e81c06f59f139870b0c932eafcefafc6 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 15 Aug 2023 18:57:10 +0300
Subject: Dump probeset summary stats
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
examples/dump-probeset-data.scm | 93 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 93 insertions(+)
create mode 100755 examples/dump-probeset-data.scm
(limited to 'examples')
diff --git a/examples/dump-probeset-data.scm b/examples/dump-probeset-data.scm
new file mode 100755
index 0000000..c4e55ab
--- /dev/null
+++ b/examples/dump-probeset-data.scm
@@ -0,0 +1,93 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+ (srfi srfi-26)
+ (ice-9 match)
+ (ice-9 regex)
+ (dump strings)
+ (dump sql)
+ (dump triples)
+ (dump special-forms))
+
+
+
+(define %connection-settings
+ (call-with-input-file (list-ref (command-line) 1)
+ read))
+
+
+
+(define-dump dump-probeset-data
+ (tables (ProbeSetXRef
+ (left-join ProbeSet "ON ProbeSet.Id = ProbeSetXRef.ProbeSetId")
+ (left-join ProbeSetFreeze "ON ProbeSet.ProbeSetFreezeId = ProbeSetFreeze.Id")))
+ "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1"
+ (schema-triples
+ (gnt:mean rdfs:domain gnc:probeset)
+ (gnt:locus rdfs:domain gnc:probeset)
+ (gnt:LRS rdfs:domain gnc:probeset)
+ (gnt:stdErr rdfs:domain gnc:probeset)
+ (gnt:stdErr rdfs:range xsd:double)
+ (gnt:pValue rdfs:domain gnc:probeset)
+ (gnt:pValue rdfs:range xsd:double)
+ (gnt:h2 rdfs:domain gnc:probeset)
+ (gnt:h2 rdfs:range xsd:double))
+ (triples (let ((id (field ("IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name))"
+ ProbeSetIdName)))
+ (probeset-id (field ProbeSet Id)))
+ (if (string-null? id)
+ (string->identifier
+ "probeset"
+ (number->string
+ probeset-id))
+ (string->identifier
+ ""
+ (regexp-substitute/global
+ #f "[^A-Za-z0-9:]"
+ id
+ 'pre "_" 'post)
+ #:separator ""
+ #:proc string-capitalize-first)))
+ (set gnt:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
+ '^^xsd:double))
+ (set gnt:locus (field PublishXRef Locus))
+ (set gnt:LRS (annotate-field
+ (field ("IFNULL(ProbeSetXRef.LRS, '')" lrs))
+ '^^xsd:double))
+ (set gnt:additive
+ (annotate-field (field ("IFNULL(ProbeSetXRef.additive, '')" additive))
+ '^^xsd:double))
+ (set gnt:stdErr (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" stdErr))
+ '^^xsd:double))
+ (set gnt:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue))
+ '^^xsd:double))
+ (set gnt:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2))
+ '^^xsd:double))
+ (set gnt:belongsToDataset
+ (string->identifier
+ ""
+ (regexp-substitute/global #f "[^A-Za-z0-9:]"
+ (field ProbeSetFreeze Name)
+ 'pre "_" 'post)
+ #:separator ""
+ #:proc string-capitalize-first))))
+
+
+
+(dump-with-documentation
+ (name "Probeset Summary Statistics")
+ (connection %connection-settings)
+ (table-metadata? #f)
+ (prefixes
+ '(("gn:" "<http://genenetwork.org/id/>")
+ ("gnc:" "<http://genenetwork.org/category/>")
+ ("gnt:" "<http://genenetwork.org/id/>")
+ ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+ ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+ ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")))
+ (inputs
+ (list dump-probeset-metadata))
+ (outputs
+ '(#:documentation "./docs/dump-probeset-summary-stats.md"
+ #:rdf "./verified-data/dump-probeset-summary-stats.ttl")))
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