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| Original file line number | Diff line number | Diff line change |
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| name: Pull request approve workflow | ||
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| on: | ||
| pull_request_review: | ||
| types: [ submitted ] | ||
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| jobs: | ||
| build: | ||
| uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop | ||
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| test: | ||
| name: "Test analysis" | ||
| uses: ./.github/workflows/test-analysis.yml | ||
| needs: build | ||
| secrets: inherit |
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61 changes: 61 additions & 0 deletions
61
cellbase-app/app/scripts/ensembl-scripts/ensembl_canonical.pl
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| #!/usr/bin/env perl | ||
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| use strict; | ||
| use Getopt::Long; | ||
| use Data::Dumper; | ||
| use JSON; | ||
| use DB_CONFIG; | ||
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| use BioMart::Initializer; | ||
| use BioMart::Query; | ||
| use BioMart::QueryRunner; | ||
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| ## Default values | ||
| my $species = 'hsapiens'; | ||
| my $outdir = "./"; | ||
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| ## Parsing command line | ||
| GetOptions ('species=s' => \$species, 'outdir=s' => \$outdir); | ||
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| my $confFile = "/opt/cellbase/scripts/ensembl-scripts/martURLLocation.xml"; | ||
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| # NB: change action to 'clean' if you wish to start a fresh configuration | ||
| # and to 'cached' if you want to skip configuration step on subsequent runs from the same registry | ||
| my $action='clean'; | ||
| my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action); | ||
| my $registry = $initializer->getRegistry; | ||
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| my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default'); | ||
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| $query->setDataset($species."_gene_ensembl"); | ||
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| $query->addAttribute("ensembl_gene_id"); | ||
| $query->addAttribute("ensembl_transcript_id"); | ||
| $query->addAttribute("transcript_is_canonical"); | ||
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| $query->formatter("TSV"); | ||
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| # Open the file for writing | ||
| open(my $fh, '>', "$outdir/ensembl_canonical.txt") or die "Cannot open ensembl_canonical.txt file: $!"; | ||
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| # Save the original stdout | ||
| my $original_stdout = *STDOUT; | ||
| open(STDOUT, '>&', $fh) or die "Can't redirect STDOUT: $!"; | ||
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| my $query_runner = BioMart::QueryRunner->new(); | ||
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| # to obtain unique rows only | ||
| $query_runner->uniqueRowsOnly(1); | ||
| $query_runner->execute($query); | ||
| #$query_runner->printHeader(); | ||
| #print ENSEMBL_CANONICAL $query_runner->printResults(); | ||
| # Call printResults which prints to STDOUT (now redirected to the file) | ||
| $query_runner->printResults(); | ||
| #$query_runner->printFooter(); | ||
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| # Restore the original stdout | ||
| open(STDOUT, '>&', $original_stdout) or die "Can't restore STDOUT: $!"; | ||
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| # Close the filehandle | ||
| close($fh) or die "Failed to close file: $!"; |
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19 changes: 19 additions & 0 deletions
19
cellbase-app/app/scripts/ensembl-scripts/martURLLocation.xml
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| <!-- | ||
| ~ Copyright 2015-2020 OpenCB | ||
| ~ | ||
| ~ Licensed under the Apache License, Version 2.0 (the "License"); | ||
| ~ you may not use this file except in compliance with the License. | ||
| ~ You may obtain a copy of the License at | ||
| ~ | ||
| ~ http://www.apache.org/licenses/LICENSE-2.0 | ||
| ~ | ||
| ~ Unless required by applicable law or agreed to in writing, software | ||
| ~ distributed under the License is distributed on an "AS IS" BASIS, | ||
| ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| ~ See the License for the specific language governing permissions and | ||
| ~ limitations under the License. | ||
| --> | ||
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| <MartRegistry> | ||
| <MartURLLocation database="ensembl_mart_111" default="1" displayName="Ensembl Genes 111" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" /> | ||
| </MartRegistry> |
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