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authorMunyoki Kilyungi2023-05-23 15:11:58 +0300
committerBonfaceKilz2023-05-26 08:40:22 +0300
commit222019fa2f85f2d63f3fd733edbe691b8d37bf4d (patch)
tree764345c1b7d7c553a8bfd23c845bec38b2253e77
parenta2a7002f629c57447b6099ac7385c5335e947e7f (diff)
downloadgn-transform-databases-222019fa2f85f2d63f3fd733edbe691b8d37bf4d.tar.gz
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>
-rwxr-xr-xexamples/dump-genotype.scm122
1 files changed, 122 insertions, 0 deletions
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")))