From 222019fa2f85f2d63f3fd733edbe691b8d37bf4d Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 23 May 2023 15:11:58 +0300
Subject: Add genotype dump

* examples/dump-genotype.scm: New dump for genotypes and their
associated datasets(that were not dumped from the info-files table).

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/dump-genotype.scm | 122 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 122 insertions(+)
 create mode 100755 examples/dump-genotype.scm

diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
new file mode 100755
index 0000000..13e4885
--- /dev/null
+++ b/examples/dump-genotype.scm
@@ -0,0 +1,122 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (rnrs programs)
+             (rnrs io ports)
+             (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-directory
+  (list-ref (command-line) 2))
+
+
+
+(define-dump dump-genofreeze
+  (tables (GenoFreeze
+           (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")
+           (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId"))
+          "WHERE GenoFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL")
+  (schema-triples
+   (gn:datasetOfInbredSet rdfs:range gn:inbredSet)
+   (gn:genotypeDataset rdfs:subPropertyOf gn:dataset)
+   (gn:shortName rdfs:range rdfs:Literal))
+  (triples (ontology
+            'dataset:
+            (regexp-substitute/global
+             #f "[^A-Za-z0-9:]"
+             (field GenoFreeze Name)
+             'pre "_" 'post))
+    (set rdf:type 'gn:genotypeDataset)
+    (set gn:name (field GenoFreeze Name))
+    (set gn:fullName (field GenoFreeze FullName))
+    (set gn:shortName (field GenoFreeze ShortName))
+    (set dct:created (annotate-field
+                      (field GenoFreeze CreateTime)
+                      '^^xsd:date))
+    (set gn:datasetOfInbredSet
+         (string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
+
+(define-dump dump-genotypes
+  (tables (Geno
+           (left-join GenoXRef "ON Geno.Id = GenoXRef.GenoId")
+           (left-join GenoFreeze "ON GenoFreeze.Id = GenoXRef.GenoFreezeId")
+           (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name")))
+  (schema-triples
+   (gn:genotypeDataset rdfs:subPropertyOf gn:dataset))
+  (triples
+      (ontology
+       'genotype:
+       (regexp-substitute/global
+        #f "[^A-Za-z0-9:]"
+        (field ("CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, ':')), Geno.Name)" abbrev))
+        'pre "_" 'post))
+    (set rdf:type 'gn:genotype)
+    (set gn:name (sanitize-rdf-string (field Geno Name)))
+    (set gn:markerName (sanitize-rdf-string (field Geno Marker_Name)))
+    (set gn:chr (field Geno Chr))
+    (set gn:mb (annotate-field (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double))
+    (set gn:sequence (annotate-field (field Geno Sequence) '^^xsd:int))
+    (set gn:source (field Geno Source))
+    (set gn:source2 (field Geno Source2))
+    (set gn:genotypeOfDataset
+         (ontology 'dataset:
+                   (regexp-substitute/global
+                    #f "[^A-Za-z0-9:]"
+                    (field GenoFreeze Name)
+                    'pre "_" 'post)))
+    (set gn:chrNum
+         (annotate-field
+          (field ("IFNULL(Geno.chr_num, '')" chr_num))
+          '^^xsd:int))
+    (set gn:comments (field ("CAST(CONVERT(BINARY CONVERT(Geno.Comments USING latin1) USING utf8) AS VARCHAR(255))" Comments)))
+    (set gn:cM
+         (annotate-field
+          (field ("IFNULL(GenoXRef.cM, '')" Chr_mm8))
+          '^^xsd:int))))
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-genotype.ttl")
+     (lambda ()
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (prefix "genotype:" "<http://genenetwork.org/genotype/>")
+       (prefix "dataset:" "<http://genenetwork.org/dataset/>")
+       (newline)
+       (dump-genofreeze db)
+       (dump-genotypes db))
+     #:encoding "utf8")))
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