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author | Munyoki Kilyungi | 2023-07-19 17:43:13 +0300 |
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committer | Munyoki Kilyungi | 2023-07-21 14:36:43 +0300 |
commit | 0b7f3cd96c1db6c535f35e73fc8126542a0301cd (patch) | |
tree | e96345b256edd89cd892b0881c6ef5932763395f /examples/dump-genotype.scm | |
parent | 50fd5b4a9f2b4c687a59ac94260ab31789aceb00 (diff) | |
download | gn-transform-databases-0b7f3cd96c1db6c535f35e73fc8126542a0301cd.tar.gz |
Dump genotypes with the new syntax
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples/dump-genotype.scm')
-rwxr-xr-x | examples/dump-genotype.scm | 119 |
1 files changed, 61 insertions, 58 deletions
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm index 1be1d34..0fbbbfe 100755 --- a/examples/dump-genotype.scm +++ b/examples/dump-genotype.scm @@ -18,9 +18,6 @@ (call-with-input-file (list-ref (command-line) 1) read)) -(define %dump-directory - (list-ref (command-line) 2)) - (define-dump dump-genofreeze @@ -29,24 +26,30 @@ (left-join InbredSet "ON GenoFreeze.InbredSetId = InbredSet.InbredSetId")) "WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL") (schema-triples - (gn:datasetOfInbredSet rdfs:range gn:inbredSet) + (gn-term: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)) + (gn-term:shortName rdfs:range rdfs:Literal)) + (triples + (string->identifier + "" + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (field GenoFreeze Name) + 'pre "_" 'post) + 'pre "_" 'post) + #:separator "" + #:proc string-capitalize-first) (set rdf:type 'gn:genotypeDataset) - (set gn:name (field GenoFreeze Name)) - (set gn:fullName (field GenoFreeze FullName)) - (set gn:shortName (field GenoFreeze ShortName)) + (set gn-term:name (field GenoFreeze Name)) + (set gn-term:fullName (field GenoFreeze FullName)) + (set gn-term:shortName (field GenoFreeze ShortName)) (set dct:created (annotate-field (field GenoFreeze CreateTime) '^^xsd:date)) - (set gn:datasetOfInbredSet - (string->identifier "inbredSet" (field InbredSet Name InbredSetName))))) + (set gn-term:datasetOfInbredSet + (string->identifier "" (field InbredSet Name InbredSetName))))) (define-dump dump-genotypes (tables (Geno @@ -54,60 +57,60 @@ (left-join GenoFreeze "ON GenoFreeze.Id = GenoXRef.GenoFreezeId") (left-join InfoFiles "ON InfoFiles.InfoPageName = GenoFreeze.Name"))) (schema-triples - (gn:genotypeDataset rdfs:subPropertyOf gn:dataset)) + (gn:genotype rdfs:range rdfs:Literal) + (gn-term:genotypeDataset rdfs:subPropertyOf gn:dataset)) (triples - (ontology - 'genotype: + (string->identifier + "" (regexp-substitute/global #f "[^A-Za-z0-9:]" (field ("CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, ':')), Geno.Name)" abbrev)) - 'pre "_" 'post)) + 'pre "_" 'post) + #:separator "" + #:proc string-capitalize-first) (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 ("IFNULL(GenoFreeze.Name, '')" DatasetName)) - 'pre "_" 'post))) - (set gn:chrNum + (set gn-term:name (sanitize-rdf-string (field Geno Name))) + (set gn-term:markerName (sanitize-rdf-string (field Geno Marker_Name))) + (set gn-term:chr (field Geno Chr)) + (set gn-term:mb (annotate-field (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double)) + (set gn-term:sequence (field Geno Sequence)) + (set gn-term:source (field Geno Source)) + (set gn-term:source2 (field Geno Source2)) + (set gn-term:genotypeOfDataset + (string->identifier + "" + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (field ("IFNULL(GenoFreeze.Name, '')" DatasetName)) + 'pre "_" 'post) + #:separator "" + #:proc string-capitalize-first) + ) + (set gn-term: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 + (set gn-term: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 "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 "owl:" "<http://www.w3.org/2002/07/owl#>") - (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") - (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 "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"))) +(dump-with-documentation + (name "Genotype Metadata") + (connection %connection-settings) + (table-metadata? #f) + (prefixes + '(("gn:" "<http://genenetwork.org/id/>") + ("gn-term:" "<http://genenetwork.org/term/>") + ("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-genofreeze + dump-genotypes)) + (outputs + '(#:documentation "./docs/dump-genotype.md" + #:rdf "./verified-data/dump-genotype.ttl"))) |