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author | Munyoki Kilyungi | 2023-08-21 14:54:21 +0300 |
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committer | Munyoki Kilyungi | 2023-08-21 14:56:57 +0300 |
commit | 51b3c0548c98e0bc05e11a89cbf6b75d31b9f8d5 (patch) | |
tree | ab3d7c6f589ed8480f0a9d451566681bcfd8eaaf /examples/dump-genotype.scm | |
parent | 849874fdfe11003f05abe5f82efde974a8c8a388 (diff) | |
download | gn-transform-databases-51b3c0548c98e0bc05e11a89cbf6b75d31b9f8d5.tar.gz |
Remove "dump-" prefix
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples/dump-genotype.scm')
-rwxr-xr-x | examples/dump-genotype.scm | 124 |
1 files changed, 0 insertions, 124 deletions
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm deleted file mode 100755 index a055039..0000000 --- a/examples/dump-genotype.scm +++ /dev/null @@ -1,124 +0,0 @@ -#! /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 (remap-species-identifiers str) - "This procedure remaps identifiers to standard binominal. Obviously this should - be sorted by correcting the database!" - (match str - ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"] - ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"] - ["Macaca mulatta" "Macaca nemestrina"] - ["Bat (Glossophaga soricina)" "Glossophaga soricina"] - [str str])) - -(define-transformer dump-genotypes - (tables (Geno - (left-join Species "USING (SpeciesId)"))) - (schema-triples - (gnc:genotype a skos:Concept) - (gnc:genotype - skos:description - "This is a set of controlled terms that are used to describe a given genotype") - (gnt:chr a owl:ObjectProperty) - (gnt:chr skos:description "This resource is located on a given chromosome") - (gnt:chr rdfs:domain gnc:genotype) - (gnt:mb a owl:ObjectProperty) - (gnt:mb skos:definition "The size of this resource in Mb") - (gnt:mb rdfs:domain gnc:genotype) - (gnt:mbMm8 a owl:ObjectProperty) - (gnt:mbMm8 skos:definition "TODO") - (gnt:mbMm8 rdfs:domain gnc:genotype) - (gnt:mb2016 a owl:ObjectProperty) - (gnt:mb2016 skos:definition "TODO") - (gnt:mb2016 rdfs:domain gnc:genotype) - (gnt:hasSequence a owl:ObjectProperty) - (gnt:hasSequence skos:definition "This resource has a given sequence") - (gnt:hasSequence rdfs:domain gnc:genotype) - (gnt:hasSource a owl:ObjectProperty) - (gnt:hasSource rdfs:domain gnc:genotype) - (gnt:hasSource skos:definition "This resource was obtained from this given source") - (gnt:hasAltSourceName a owl:ObjectProperty) - (gnt:hasAltSourceName rdfs:domain gnc:genotype) - (gnt:hasAltSourceName - skos:definition - "The alternative name this resource was obtained from") - (gnt:chrNum a owl:ObjectProperty) - (gnt:chrNum rdfs:domain gnc:genotype) - (gnt:chrNum skos:definition "The chromosome number for this resource") - (gnt:chrNum skos:definition "The chromosome number for this resource")) - (triples - (string->identifier - "" - (regexp-substitute/global - #f "[^A-Za-z0-9:]" - (field Geno Name) - 'pre "_" 'post) - #:separator "" - #:proc string-capitalize-first) - (set rdf:type 'gnc:genotype) - (set skos:prefLabel (sanitize-rdf-string (field Geno Name))) - (set gnt:chr (field Geno Chr)) - (set gnt:mb (annotate-field - (field ("IFNULL(Geno.Mb, '')" Mb)) '^^xsd:double)) - (set gnt:mbMm8 (annotate-field (field ("IFNULL(Geno.Mb_mm8, '')" Mb_mm8)) - '^^xsd:double)) - (set gnt:mb2016 - (annotate-field (field ("IFNULL(Geno.Mb_2016, '')" Mb_2016)) - '^^xsd:double)) - (set gnt:hasSequence (field Geno Sequence)) - (set gnt:hasSource (field Geno Source)) - ;; Only dump Source2 if it differs from Source - (set gnt:hasAltSourceName - (field ("IF((Source2 = Source), NULL, Source2)" - Source2))) - (set gnt:belongsToSpecies - (string->identifier - "" (remap-species-identifiers (field Species Fullname)) - #:separator "" - #:proc string-capitalize-first)) - (set gnt:chrNum - (annotate-field - (field Geno chr_num) - '^^xsd:int)) - (set rdfs:comments (field Geno Comments)))) - - - -(dump-with-documentation - (name "Genotype Metadata") - (connection %connection-settings) - (table-metadata? #f) - (prefixes - '(("dct:" "<http://purl.org/dc/terms/>") - ("gn:" "<http://genenetwork.org/id/>") - ("gnc:" "<http://genenetwork.org/category/>") - ("gnt:" "<http://genenetwork.org/term/>") - ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") - ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") - ("owl:" "<http://www.w3.org/2002/07/owl#>") - ("skos:" "<http://www.w3.org/2004/02/skos/core#>") - ("xsd:" "<http://www.w3.org/2001/XMLSchema#>"))) - (inputs - (list dump-genotypes)) - (outputs - '(#:documentation "./docs/dump-genotype.md" - #:rdf "/export/data/genenetwork-virtuoso/dump-genotype.ttl"))) |