Skip to content

Latest commit

 

History

History
91 lines (66 loc) · 3.48 KB

Xref_GPR.md

File metadata and controls

91 lines (66 loc) · 3.48 KB

Xref_GPR

Module Bio::EnsEMBL::EGPipeline::PipeConfig::Xref_GPR_conf

Adding [metabolic reaction annotations from the Gramene Plant Reactome project to plant genes as xrefs

Prerequisites

A registry file with the locations of the core database server(s) and the production database (or -production_db $PROD_DB_URL specified).

Reactome flat files (see below).

How to run

init_pipeline.pl Bio::EnsEMBL::EGPipeline::PipeConfig::Xref_GPR_conf \
    $($CMD details script) \
    -hive_force_init 1\
    -registry $REG_FILE \
    -xref_reac_file Ensembl2PlantReactomeReactions.txt \
    -xref_path_file Ensembl2PlantReactome.txt \
    ${OTHER_OPTIONS} \
    2> $OUT_DIR/init.stderr \
    1> $OUT_DIR/init.stdout

SYNC_CMD=$(cat $OUT_DIR/init.stdout | grep -- -sync'$' | perl -pe 's/^\s*//; s/"//g')
# should get something like
#   beekeeper.pl -url $url -sync

LOOP_CMD=$(cat $OUT_DIR/init.stdout | grep -- -loop | perl -pe 's/^\s*//; s/\s*#.*$//; s/"//g')
# should get something like
#   beekeeper.pl -url $url -reg_file $REG_FILE -loop

$SYNC_CMD 2> $OUT_DIR/sync.stderr 1> $OUT_DIR/sync.stdout
$LOOP_CMD 2> $OUT_DIR/loop.stderr 1> $OUT_DIR/loop.stdout

Parameters / Options

option default value meaning
-species species to process, several -species options are possible
-pipeline_dir directory to store results to
-xref_reac_file flat file with Gramene Plant Reactome reactions data
-xref_path_file flat file with Gramene Plant Reactome pathways data
-uppercase_gene_id 0 use uppercased versions of stable IDs for mapping; 1 -- to uppercase
-production_lookup 1 Fetch analysis display name, description and web data from the production database; 0 -- to disable

Notes

The pipeline is designed to be run using Ensembl/plant_tools add_gramene_reactome.pl script.

Please, see Ensembl/plant_tools on how to setup, etc.

Here's the example scenario of usage.

  1. Get reactome flat files:
wget -c https://plantreactome.gramene.org/download/current/Ensembl2PlantReactomeReactions.txt
wget -c https://plantreactome.gramene.org/download/current/Ensembl2PlantReactome.txt
  1. Load xrefs using the script itself:
ENS_ROOT_DIR=$(pwd) # path to the ensembl repos
ENS_VERSION=104 # or whatever

PIPELINE_DIR=$(pwd)/pipeline_out  # whatever, dir to store intermediate results
mkdir -p ${PIPELINE_DIR}

${ENS_ROOT_DIR}/plant_tools/production/core/add_gramene_reactome.pl
    -v ${ENS_VERSION} \
    -R ${REG_FILE} \
    -P ${PIPELINE_DIR} \
    -reactions Ensembl2PlantReactomeReactions.txt \
    -pathways Ensembl2PlantReactome.txt \
    -s triticum_turgidum \
    -w

Sometimes you neef to pass -uppercase_gene_id 1 option to the underlying pipeline to allow usage of uppercase gene stable IDs for mapping (i.e. for Oryza sativa (rice))

  1. Make sure you have a proper analysis_description entry in you database(s).

Parts

A few generic from Common::RunnableDB.

A few from Xref.