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author | Munyoki Kilyungi | 2023-05-23 15:11:58 +0300 |
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committer | BonfaceKilz | 2023-05-26 08:40:22 +0300 |
commit | 222019fa2f85f2d63f3fd733edbe691b8d37bf4d (patch) | |
tree | 764345c1b7d7c553a8bfd23c845bec38b2253e77 /examples/dump-genotype.scm | |
parent | a2a7002f629c57447b6099ac7385c5335e947e7f (diff) | |
download | gn-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>
Diffstat (limited to 'examples/dump-genotype.scm')
-rwxr-xr-x | examples/dump-genotype.scm | 122 |
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"))) |