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Biomart mappings testable by species and less of Atlas Prod env var (#6)
* Initial changes, wip still * Makes bioentities properties configurable for ensemblUpdate * Allows reuse of ontology files for faster testing (not by default) * Allows setting interpro version * More ATLAS_PROD removal * Removes unused imports * Avoids ATLAS_PROD variable usage in PropertiesAdequate * Avoids hardcoded paths for Directories, makes experiments paths configurable. * Adds example testing directory structure * Some documentation * Avoids ATLAS_PROD env var * More documentation * Makes annotation sources configurable * Main method for mapping validation only * Adds env dockerfile * Missing default y for apt-get install * Jenkins k8s integration seems to be mounting stuff on /usr/local/bin (ouch!) * Exits with error code on bad validation test. * Revert "Jenkins k8s integration seems to be mounting stuff on /usr/local/bin (ouch!)" This reverts commit 7214272. * Change connection protocol of E! sites to HTTPS * Updates documentation a bit. * Exports PATH_BIOENTITTY.... * Add TODO to handle correctly missing dataset error. * Adds explanation on how to use ANNOTATION_SOURCES
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FROM lolhens/ammonite:latest | ||
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RUN apt-get update -y && apt-get install -y git |
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#!/bin/bash | ||
#!/usr/bin/env bash | ||
# This script retrieves the latest mapping between GO ids and terms | ||
# Author: [email protected], [email protected] | ||
set -euo pipefail | ||
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PROJECT_ROOT=`dirname $0`/../.. | ||
export JAVA_OPTS=-Xmx3000M | ||
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# To avoid using the depths functionality, set env var $GET_GO_DEPTHS to something different to "yes". | ||
GET_GO_DEPTHS=${GET_GO_DEPTHS:-"yes"} | ||
USE_EXITING_ONTOLOGY_FILES=${USE_EXISTING_ONTOLOGY_FILES:-"no"} | ||
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IFS=" | ||
" | ||
outputDir=$1 | ||
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@@ -13,8 +19,10 @@ if [[ -z "$outputDir" ]]; then | |
fi | ||
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echo "Fetching GO and PO owl files" | ||
curl -s "http://geneontology.org/ontology/go.owl" > $outputDir/go.owl | ||
curl -s "http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/plant_ontology.owl?view=co" > $outputDir/po.owl | ||
if [ $USE_EXISTING_ONTOLOGY_FILES == "no" ]; then | ||
curl -s "http://geneontology.org/ontology/go.owl" > $outputDir/go.owl | ||
curl -s "http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/plant_ontology.owl?view=co" > $outputDir/po.owl | ||
fi | ||
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echo "Extracting GO id -> term" | ||
amm -s $PROJECT_ROOT/src/go/PropertiesFromOwlFile.sc terms $outputDir/go.owl \ | ||
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@@ -62,7 +70,13 @@ from | |
group by go_id, ancestor_id;" | sqlplus goselect/selectgo@goapro | grep '^GO:' | sort -t$'\t' -rk2,2 | awk -F"\t" '{ print $1"\t"$2+1 }' | sort -buk1,1 | ||
} | ||
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get_ontology_id2Depth_mappings > $outputDir/goIDToDepth.tsv | ||
if [ $GET_GO_DEPTHS == "yes" ]; then | ||
get_ontology_id2Depth_mappings > $outputDir/goIDToDepth.tsv | ||
else | ||
# write file with just zero depths | ||
echo "As requested, ignoring GO depths and writing dummy file with all depths 0 based on $outputDir/goIDToTerm.tsv ." | ||
awk -F'\t' '{ print $1"\t0" }' $outputDir/goIDToTerm.tsv > $outputDir/goIDToDepth.tsv | ||
fi | ||
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# Append Plant Ontology terms at the end of the Gene Ontology file (Ensembl provides Plant Ontology (PO) and Gene Ontology (GO) terms - as GO terms) | ||
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#!/usr/bin/env bash | ||
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# This script retrieves the latest mapping between Interpro ids and their types (family/domain) and terms | ||
# Author: [email protected] | ||
PROJECT_ROOT=`dirname $0`/../.. | ||
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@@ -8,8 +10,10 @@ if [[ -z "$outputDir" ]]; then | |
exit 1 | ||
fi | ||
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curl -s ftp://ftp.ebi.ac.uk/pub/databases/interpro/62.0/interpro.xml.gz | zcat > $outputDir/interpro.xml | ||
curl -s ftp://ftp.ebi.ac.uk/pub/databases/interpro/62.0/interpro.dtd > $outputDir/interpro.dtd | ||
INTERPRO_VERSION=${INTERPRO_VERSION:-"62.0"} | ||
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curl -s ftp://ftp.ebi.ac.uk/pub/databases/interpro/$INTERPRO_VERSION/interpro.xml.gz | zcat > $outputDir/interpro.xml | ||
curl -s ftp://ftp.ebi.ac.uk/pub/databases/interpro/$INTERPRO_VERSION/interpro.dtd > $outputDir/interpro.dtd | ||
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pushd $PROJECT_ROOT | ||
echo "Parse the file we obtained from Interpro's FTP site" | ||
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